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Conserved domains on  [gi|226442897|ref|NP_001140168|]
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lysine-specific demethylase 4C isoform 4 [Homo sapiens]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 10338146)

PHD (plant homeodomain) finger domain-containing protein contains a C4HC3 zinc-finger-like motif

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_JMJD2C cd15577
PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed ...
 666-768 9.72e-61

PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications through modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


:

Pssm-ID: 277052  Cd Length: 104  Bit Score: 200.44  E-value: 9.72e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 666 HCAICTLLMPYHKPDSSNEENDARWET-KLDEVVTSEGKTKPLIPEMCFIYSEENIEYSPPNAFLEEDGTSLLISCAKCC 744
Cdd:cd15577    1 HCAICTLFMPYYKPDALNEENSAQWEMeLPAAPCISMRKTKPLIPEMCFIYREENCEPSPPNALLQEDGTSLLISCAKCC 80

                         90       100
                 ....*....|....*....|....
gi 226442897 745 VRVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15577   81 VQVHASCYGVPSHEIHDGWLCARC 104
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 199-315 4.26e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


:

Pssm-ID: 396791  Cd Length: 114  Bit Score: 177.11  E-value: 4.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897  199 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQgffPSSSQGCDAFLRHKMTLISPSVLKKYG 278
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 226442897  279 IPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 315
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 777-830 3.81e-31

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15715:

Pssm-ID: 473978  Cd Length: 110  Bit Score: 117.75  E-value: 3.81e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15715    1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKL 54
JmjN super family cl15840
jmjN domain;
38-79 1.05e-10

jmjN domain;


The actual alignment was detected with superfamily member smart00545:

Pssm-ID: 472837  Cd Length: 42  Bit Score: 57.27  E-value: 1.05e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 226442897    38 IMTFRPSMEEFREFNKYLAYMESKgAHRAGLAKVIPPKEWKP 79
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
 
Name Accession Description Interval E-value
PHD_JMJD2C cd15577
PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed ...
 666-768 9.72e-61

PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications through modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277052  Cd Length: 104  Bit Score: 200.44  E-value: 9.72e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 666 HCAICTLLMPYHKPDSSNEENDARWET-KLDEVVTSEGKTKPLIPEMCFIYSEENIEYSPPNAFLEEDGTSLLISCAKCC 744
Cdd:cd15577    1 HCAICTLFMPYYKPDALNEENSAQWEMeLPAAPCISMRKTKPLIPEMCFIYREENCEPSPPNALLQEDGTSLLISCAKCC 80

                         90       100
                 ....*....|....*....|....
gi 226442897 745 VRVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15577   81 VQVHASCYGVPSHEIHDGWLCARC 104
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 199-315 4.26e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 177.11  E-value: 4.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897  199 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQgffPSSSQGCDAFLRHKMTLISPSVLKKYG 278
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 226442897  279 IPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 315
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 777-830 3.81e-31

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 117.75  E-value: 3.81e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15715    1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKL 54
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
775-830 8.96e-24

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 96.64  E-value: 8.96e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 226442897  775 AECCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:pfam13832   1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKL 56
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
730-831 8.12e-15

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 78.49  E-value: 8.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 730 EEDGTSLLISCAKCCVRVHASCYGIPshEICDG-WLCARCKRNAWTAECCL-CNLRGGALKQTKNNKWAHVMCAVAVPEV 807
Cdd:COG5141  203 HNENSNAIVFCDGCEICVHQSCYGIQ--FLPEGfWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPEL 280

                         90       100
                 ....*....|....*....|....*
gi 226442897 808 RFTNVPERTQID-VGRIPLQRLKLG 831
Cdd:COG5141  281 SFGHLLSKDPIDnIASVSSSRWKLG 305
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 734-768 1.78e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 65.05  E-value: 1.78e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 226442897  734 TSLLISCAKCCVRVHASCYGIPSHEICDGWLCARC 768
Cdd:pfam13831   1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 170-229 4.69e-13

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 64.20  E-value: 4.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 226442897   170 DEWNIARLNTVLDVVEEeCGISIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 229
Cdd:smart00558   1 QLWNLAKLPFKLNLLSD-LPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 38-79 1.05e-10

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 57.27  E-value: 1.05e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 226442897    38 IMTFRPSMEEFREFNKYLAYMESKgAHRAGLAKVIPPKEWKP 79
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
JmjN pfam02375
jmjN domain;
39-73 5.30e-10

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 54.99  E-value: 5.30e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 226442897   39 MTFRPSMEEFREFNKYLAYMESKGAhRAGLAKVIP 73
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 730-768 2.76e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 44.90  E-value: 2.76e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 226442897   730 EEDGTSLLISCAKCCVRVHASCYGIPSHEI--CDGWLCARC 768
Cdd:smart00249   7 KPDDGGELLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
 
Name Accession Description Interval E-value
PHD_JMJD2C cd15577
PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed ...
 666-768 9.72e-61

PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications through modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277052  Cd Length: 104  Bit Score: 200.44  E-value: 9.72e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 666 HCAICTLLMPYHKPDSSNEENDARWET-KLDEVVTSEGKTKPLIPEMCFIYSEENIEYSPPNAFLEEDGTSLLISCAKCC 744
Cdd:cd15577    1 HCAICTLFMPYYKPDALNEENSAQWEMeLPAAPCISMRKTKPLIPEMCFIYREENCEPSPPNALLQEDGTSLLISCAKCC 80

                         90       100
                 ....*....|....*....|....
gi 226442897 745 VRVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15577   81 VQVHASCYGVPSHEIHDGWLCARC 104
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 199-315 4.26e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 177.11  E-value: 4.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897  199 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQgffPSSSQGCDAFLRHKMTLISPSVLKKYG 278
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 226442897  279 IPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 315
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 777-830 3.81e-31

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 117.75  E-value: 3.81e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15715    1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKL 54
PHD_JMJD2A cd15575
PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed ...
 666-768 2.77e-30

PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277050  Cd Length: 100  Bit Score: 115.00  E-value: 2.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 666 HCAICTLLMPYHKPDSSNEENDARWETKLdevVTSEGKTKPLIPEMCFIYSEENIEYSPPNAFLEEDGTSLLISCAKCCV 745
Cdd:cd15575    1 HCAVCMLFQTYQVDCWGGHNSSSGVAASE---ARIKKKTKPLIPEMCFTSTGCNTDLNLSTPYLEEDGTSILVTCKKCCV 77

                         90       100
                 ....*....|....*....|...
gi 226442897 746 RVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15575   78 CVHASCYGVSPEKAAEDWMCSRC 100
PHD_JMJD2B cd15576
PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed ...
 666-768 9.37e-30

PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277051  Cd Length: 99  Bit Score: 113.46  E-value: 9.37e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 666 HCAICTLLMPYHKpdssNEENDARWETKLDEVVTSEGKTKPLIPEMCFIYSEENIEYSPPNAFLEEDGTSLLISCAKCCV 745
Cdd:cd15576    1 YCAICTLFYPYTQ----SLQDPKEISDMSGLVSKVGQKTRPLIPEMCFTAGGENTEPLPSNSYIGDDGTSVLLSCAKCCL 76

                         90       100
                 ....*....|....*....|...
gi 226442897 746 RVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15576   77 QVHASCYGVNPDLVNEGWTCSRC 99
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 777-830 8.32e-28

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 108.22  E-value: 8.32e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15675    1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPARLKL 54
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
775-830 8.96e-24

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 96.64  E-value: 8.96e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 226442897  775 AECCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:pfam13832   1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKL 56
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 777-830 3.11e-21

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 89.65  E-value: 3.11e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15713    1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKL 54
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 777-830 2.75e-20

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 86.91  E-value: 2.75e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15714    1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKL 54
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
730-831 8.12e-15

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 78.49  E-value: 8.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 730 EEDGTSLLISCAKCCVRVHASCYGIPshEICDG-WLCARCKRNAWTAECCL-CNLRGGALKQTKNNKWAHVMCAVAVPEV 807
Cdd:COG5141  203 HNENSNAIVFCDGCEICVHQSCYGIQ--FLPEGfWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPEL 280

                         90       100
                 ....*....|....*....|....*
gi 226442897 808 RFTNVPERTQID-VGRIPLQRLKLG 831
Cdd:COG5141  281 SFGHLLSKDPIDnIASVSSSRWKLG 305
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 734-768 1.78e-13

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 65.05  E-value: 1.78e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 226442897  734 TSLLISCAKCCVRVHASCYGIPSHEICDGWLCARC 768
Cdd:pfam13831   1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 170-229 4.69e-13

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 64.20  E-value: 4.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 226442897   170 DEWNIARLNTVLDVVEEeCGISIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 229
Cdd:smart00558   1 QLWNLAKLPFKLNLLSD-LPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 777-830 8.47e-13

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 65.43  E-value: 8.47e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQID-VGRIPLQRLKL 830
Cdd:cd15670    1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDgIQNIPKARWKL 55
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 777-830 2.23e-11

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 61.45  E-value: 2.23e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 226442897 777 CCLCNLRGGALKQ------TKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRLKL 830
Cdd:cd15571    1 CALCPRSGGALKGggalktTSDGLWVHVVCALWSPEVYFDDGTLLEVEGVSKIPKRRKKL 60
PHD_JMJD2 cd15493
PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; ...
 737-768 2.95e-11

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. This model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276968  Cd Length: 42  Bit Score: 58.86  E-value: 2.95e-11
                         10        20        30
                 ....*....|....*....|....*....|...
gi 226442897 737 LISCAKCCVRVHASCYGIPSHE-ICDGWLCARC 768
Cdd:cd15493   10 LLVCSRCCVCVHASCYGVPDIPgDGEGWKCDRC 42
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 38-79 1.05e-10

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 57.27  E-value: 1.05e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 226442897    38 IMTFRPSMEEFREFNKYLAYMESKgAHRAGLAKVIPPKEWKP 79
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
ePHD_AF10_like cd15672
Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) ...
 777-827 1.62e-10

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.


Pssm-ID: 277142  Cd Length: 116  Bit Score: 59.01  E-value: 1.62e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQR 827
Cdd:cd15672    1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPIILQDVPQDR 51
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 777-830 5.07e-10

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 57.78  E-value: 5.07e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQID-VGRIPLQRLKL 830
Cdd:cd15701    1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDsIEHIPPARWKL 55
JmjN pfam02375
jmjN domain;
39-73 5.30e-10

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 54.99  E-value: 5.30e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 226442897   39 MTFRPSMEEFREFNKYLAYMESKGAhRAGLAKVIP 73
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 777-830 6.70e-10

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277172  Cd Length: 118  Bit Score: 57.36  E-value: 6.70e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQID-VGRIPLQRLKL 830
Cdd:cd15702    1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKL 55
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 777-830 1.02e-09

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 56.99  E-value: 1.02e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQID-VGRIPLQRLKL 830
Cdd:cd15703    1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEgVNNIPPARWKL 55
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 777-830 2.63e-09

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 55.53  E-value: 2.63e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226442897 777 CCLCNLRGGALKQTKN-NKWAHVMCAVAVPEVRFTNvPERTQ--IDVGRIPLQRLKL 830
Cdd:cd15671    1 CVLCPKKGGAMKSTKSgTKWVHVSCALWIPEVSIGC-PEKMEpiTKISHIPMSRWAL 56
ePHD_AF10 cd15708
Extended PHD finger found in protein AF-10 and similar proteins; The extended plant ...
 777-827 1.66e-08

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.


Pssm-ID: 277178  Cd Length: 129  Bit Score: 53.93  E-value: 1.66e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQR 827
Cdd:cd15708    5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIVLQSVPHER 55
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 777-812 5.39e-07

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and this non-canonical ePHD finger. It can interact with histones through its PHD fingers.


Pssm-ID: 277144  Cd Length: 114  Bit Score: 48.92  E-value: 5.39e-07
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNV 812
Cdd:cd15674    1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDV 36
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 777-830 6.80e-07

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 48.62  E-value: 6.80e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQID-VGRIPLQRLKL 830
Cdd:cd15662    1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDgINAISKERWEL 55
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
 777-827 8.91e-07

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.


Pssm-ID: 277133  Cd Length: 112  Bit Score: 48.28  E-value: 8.91e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226442897 777 CCLCNLRGGALKQTK-NNKWAHVMCAVAVPEVRFTNVpERTQIDVG--RIPLQR 827
Cdd:cd15663    1 CCLCPVKGGALKPTDvEGLWVHVTCAWFRPEVCFKNE-EKMEPAVGllRIPLST 53
ePHD_AF17 cd15709
Extended PHD finger found in protein AF-17 and similar proteins; The extended plant ...
 777-828 9.54e-07

Extended PHD finger found in protein AF-17 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger.


Pssm-ID: 277179  Cd Length: 125  Bit Score: 48.52  E-value: 9.54e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 226442897 777 CCLCNLRGGALKQTKNNKWAHVMCAVAVPEVRFTNVPERTQIDVGRIPLQRL 828
Cdd:cd15709    5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIVLQYVPHDRF 56
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 777-830 1.96e-06

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 47.41  E-value: 1.96e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226442897 777 CCLCNLRGGALKQTK-NNKWAHVMCAVAVPEVRFTnVPERTQ--IDVGRIPLQRLKL 830
Cdd:cd15706    1 CLLCPKTGGAMKATRtGTKWAHVSCALWIPEVSIA-CPERMEpiTKVSHIPPSRWAL 56
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 730-768 2.76e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 44.90  E-value: 2.76e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 226442897   730 EEDGTSLLISCAKCCVRVHASCYGIPSHEI--CDGWLCARC 768
Cdd:smart00249   7 KPDDGGELLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 777-830 3.15e-06

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277175  Cd Length: 111  Bit Score: 46.63  E-value: 3.15e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226442897 777 CCLCNLRGGALKQTKN-NKWAHVMCAVAVPEVRFtNVPERTQ--IDVGRIPLQRLKL 830
Cdd:cd15705    1 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSI-GCPEKMEpiTKISHIPASRWAL 56
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 777-830 6.63e-06

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 45.66  E-value: 6.63e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 226442897 777 CCLCNLRGGALKQTKN-NKWAHVMCAVAVPEVRFTNVPERTQI-DVGRIPLQRLKL 830
Cdd:cd15707    1 CILCPNKGGAMKSTRSgTKWAHVSCALWIPEVSIGCVEKMEPItKISSIPASRWAL 56
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
 730-768 8.39e-05

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 40.82  E-value: 8.39e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 226442897 730 EEDGTSLLISCAKCCVRVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15495    9 EDDDNNPLITCNRCQISVHQKCYGIREVDPDGSWVCRAC 47
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 737-768 2.80e-04

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 39.14  E-value: 2.80e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 226442897 737 LISCAKCCVRVHASCYGIPSheICDG-WLCARC 768
Cdd:cd15492   16 IVFCDGCNVAVHQSCYGIPL--IPEGdWFCRKC 46
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 728-768 4.59e-04

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 38.45  E-value: 4.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 226442897 728 FLEEDGtsLLISCAKCCVRVHASCYGIPSHEICDGWLCARC 768
Cdd:cd15550    6 FEHDDG--FMICCDKCSVWQHGDCMGIDRENIPDSYLCEQC 44
ePHD_Snt2p_like cd15667
Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) ...
 777-818 6.02e-04

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.


Pssm-ID: 277137  Cd Length: 141  Bit Score: 40.83  E-value: 6.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226442897 777 CCLCNLRGG---------------ALKQTKNNKWAHVMCAVAVPEVRFTNvPERTQI 818
Cdd:cd15667    1 CSLCNAKESnyelakkqsprtrpdALKCTSNGTWCHVLCALFNEDIKFGN-SKSLQP 56
ePHD_JADE1 cd15704
Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant ...
 776-830 6.45e-04

Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the Serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation and ASA transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277174  Cd Length: 118  Bit Score: 40.44  E-value: 6.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 226442897 776 ECCLCNLRGGALKQTKN-NKWAHVMCAVAVPEVRFTNvPERTQ--IDVGRIPLQRLKL 830
Cdd:cd15704    3 KCLLCPKKGGAMKPTRSgTKWVHVSCALWIPEVSIGS-PEKMEpiTKVSHIPSSRWAL 59
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 732-768 6.78e-04

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 38.07  E-value: 6.78e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 226442897 732 DGTSLLISCAKCCVRVHASCYGIPSHEIC--DGWLCARC 768
Cdd:cd15489   10 DLGGELLQCDGCGKWFHADCLGPPLSSFVpnGKWICPVC 48
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 730-770 1.33e-03

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 37.47  E-value: 1.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 226442897  730 EEDGTSLLISCAKCCVRVHASCYGIP--SHEICDG-WLCARCKR 770
Cdd:pfam00628   7 KSDDGGELVQCDGCDDWFHLACLGPPldPAEIPSGeWLCPECKP 50
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
 730-768 5.10e-03

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 35.82  E-value: 5.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 226442897 730 EEDGtSLLISCAKCCVRVHASCYGIP-SHEICDGWLCARC 768
Cdd:cd15556    8 DDDG-ERMIACDVCEVWQHTRCVGIAdNEEPPDHFLCRRC 46
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 730-768 8.72e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 35.28  E-value: 8.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 226442897 730 EEDGTSLLISCAKCCVRVHASCYGIPSheICDG-WLCARC 768
Cdd:cd15572   11 ECQNSNVILFCDMCNLAVHQECYGVPY--IPEGqWLCRRC 48
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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