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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKGLGAAIQCHKVNCYTAF 348
Cdd:cd15703      1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCKQKGRGAAIQCHKVNCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403  349 HVTCAQRAGLFMKIEPMRETSLNGTIFTVRKTAYCEAH 386
Cdd:cd15703     81 HVTCAQRAGLFMKIEPVRETGLNGTTFTVRKTAYCENH 118

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 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 a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1075 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 1154
Cdd:cd20158      1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403 1155 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 1192
Cdd:cd20158     81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKGLGAAIQCHKVNCYTAF 348
Cdd:cd15703      1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCKQKGRGAAIQCHKVNCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403  349 HVTCAQRAGLFMKIEPMRETSLNGTIFTVRKTAYCEAH 386
Cdd:cd15703     81 HVTCAQRAGLFMKIEPVRETGLNGTTFTVRKTAYCENH 118

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 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 a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1075 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 1154
Cdd:cd20158      1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403 1155 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 1192
Cdd:cd20158     81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

PHD-zinc-finger like domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  267 VDCVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIeGIDNIPPARWKLTCYICKQKGlGAAIQCHKVNCYT 346
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPI-DVSRIPPERWKLKCVFCKKRS-GACIQCSKGRCTT 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1511976403  347 AFHVTCAQRAGLFMKIEpmretslngTIFTVRKTAYCEAH 386
Cdd:pfam13832   79 AFHVTCAQAAGVYMEPE---------DWPNVVVIAYCQKH 109

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1511976403  212 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCCLQSPSR 265
Cdd:cd15572      1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSR 54

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  599 LRTTLDLLQEKDPAHIFAEPVNLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHR 678
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ....
gi 1511976403  679 AAVR 682
Cdd:pfam00439   81 AAEK 84

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1079 ELVWAKCRGYPSYPALIIDPKMPREGLLHNGvpipvppldvlklgeqkqaeAGEKLFLVLFFDNKRTwQWLPRDKVLPLG 1158
Cdd:pfam00855    2 DLVWAKLKGYPWWPARVVDPEELPENVLKPK--------------------KKDGEYLVRFFGDSEF-AWVKPKDLKPFD 60

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1511976403 1159 VEDTVDKLKMleGRKTSIRKSVQVAYDRAMIHLS 1192
Cdd:pfam00855   61 EGDEFEYLKK--KKKKKKKKAFKKALEEAEEALK 92

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.

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1511976403   214 FCCVCldDECHNSNVILFCDICNLAVHQECYGVPY---IPEGQWLC-RC 258
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLleeEPDGKWYCpKC 47

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKGLGAAIQCHKVNCYTAF 348
Cdd:cd15703      1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCKQKGRGAAIQCHKVNCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403  349 HVTCAQRAGLFMKIEPMRETSLNGTIFTVRKTAYCEAH 386
Cdd:cd15703     81 HVTCAQRAGLFMKIEPVRETGLNGTTFTVRKTAYCENH 118

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 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 a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1075 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 1154
Cdd:cd20158      1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1511976403 1155 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 1192
Cdd:cd20158     81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKGLGAAIQCHKVNCYTAF 348
Cdd:cd15701      1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRGSGACIQCHKANCYTAF 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1511976403  349 HVTCAQRAGLFMKIEPMRETSLNGTIFTVRKTAYCEAHSPP 389
Cdd:cd15701     81 HVTCAQQAGLYMKMEPVRETGANGTSFSVRKTAYCDIHTPP 121

PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also called 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 extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1075 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 1154
Cdd:cd20157      1 LEPLKVVWAKCSGYPSYPALIIDPKMPRVGCHHNGVTIPVPPLDVLKIGEQMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1511976403 1155 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLSRV 1194
Cdd:cd20157     81 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 120

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  594 PFNVLLRTTLDLLQEKDPAHIFAEPVNLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKD 673
Cdd:cd05512      1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80

                           90
                   ....*....|....*...
gi 1511976403  674 TIFHRAAVRLRDLGGAIL 691
Cdd:cd05512     81 TIFYRAAVRLRDQGGAIL 98

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of 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 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403 1075 LEPLELVWAKCRGYPSYPALIIDPKMPREGllhNGVPIPVPPLDVLKlgeqkqaEAGEKLFLVLFFDNKRTWQWLPRDKV 1154
Cdd:cd05839      1 LEPGDLVWAKCRGYPWYPAEIVDPKDPKEG---NGVPIPVPPDRVLK-------KSNEKLYLVLFFDAKRTWGWLPRNKL 70

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1511976403 1155 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIH 1190
Cdd:cd05839     71 RPLGVDEELDKLKLSEAKKSKRRKEVRKAYERACKH 106

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQ------TSDGHWAHVVCAIWIPEVCFANTVFLEpIEGIDNIPPARWKLTCYICKQKGlGAAIQCHKV 342
Cdd:cd15571      1 CALCPRSGGALKGggalktTSDGLWVHVVCALWSPEVYFDDGTLLE-VEGVSKIPKRRKKLKCSICGKRG-GACIQCSYP 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1511976403  343 NCYTAFHVTCAQRAGLFMKIEPMREtslngtiftvRKTAYCEAH 386
Cdd:cd15571     79 GCPRSFHVSCAIRAGCLFEFEDGPG----------NFVVYCPKH 112

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1511976403  212 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCCLQSPSR 265
Cdd:cd15572      1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSR 54

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403   588 MELELMPFNVLLRTTLDLLQEKDPAHIFAEPVNLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCM 667
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 1511976403   668 KYNAKDTIFHRAAVRLRDLGGAILRHA 694
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDG-HWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKgLGAAIQCHKVNCYTA 347
Cdd:cd15707      1 CILCPNKGGAMKSTRSGtKWAHVSCALWIPEVSIGCVEKMEPITKISSIPASRWALICVLCRER-TGACIQCSVKTCKTA 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1511976403  348 FHVTCAQRAGLFMK--IEPMRETSlngtiftVRKTAYCEAH 386
Cdd:cd15707     80 YHVTCGFQHGLEMKtiLDEESEDG-------VKLRSYCQKH 113

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEgIDNIPPARWKLTCYICKQ-----KGLGAAIQCHKVN 343
Cdd:cd15675      1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPID-ISKIPPARLKLKCIYCSKitksmSHMGACIQCSTGK 79

                           90       100
                   ....*....|....*....|.
gi 1511976403  344 CYTAFHVTCAQRAGlfMKIEP 364
Cdd:cd15675     80 CTTSFHVTCAHAAG--VQMEP 98

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, 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 canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1511976403  212 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCCLQSPSR 265
Cdd:cd15677      1 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRSR 54

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDG-HWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKgLGAAIQCHKVNCYTA 347
Cdd:cd15706      1 CLLCPKTGGAMKATRTGtKWAHVSCALWIPEVSIACPERMEPITKVSHIPPSRWALVCSLCKLK-TGACIQCSVKSCITA 79

                           90
                   ....*....|....
gi 1511976403  348 FHVTCAQRAGLFMK 361
Cdd:cd15706     80 FHVTCAFEHSLEMK 93

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  595 FNVLLRTTLDLLQEK--DPAHIFAEPVNLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAK 672
Cdd:cd04369      1 LKKKLRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                           90
                   ....*....|....
gi 1511976403  673 DTIFHRAAVRLRDL 686
Cdd:cd04369     81 GSPIYKDAKKLEKL 94

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  267 VDCVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEgIDNIPPARWKLTCYICKQKG------LGAAIQCH 340
Cdd:cd15708      3 VRCELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIV-LQSVPHERYNKTCYICDEQGreskaaTGACMTCN 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1511976403  341 KVNCYTAFHVTCAQRAGLFMkiepmrETSLNGTIfTVRKTAYCEAH 386
Cdd:cd15708     82 KHGCRQAFHVTCAQLAGLLC------EEEGNGAD-NVQYCGYCKYH 120

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTS-DGHWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKGlGAAIQCHKvnCYTA 347
Cdd:cd15663      1 CCLCPVKGGALKPTDvEGLWVHVTCAWFRPEVCFKNEEKMEPAVGLLRIPLSTFLKACVICKQIH-GSCTQCCK--CATY 77

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1511976403  348 FHVTCAQRAGLFMKIEPMREtslNGtIFTVRKTAYCEAH 386
Cdd:cd15663     78 FHAMCASRAGYHMELHCLEK---NG-VQITRMVSYCSFH 112

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1511976403  214 FCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCC 259
Cdd:cd15492      1 VCDVCLDGESEDDNEIVFCDGCNVAVHQSCYGIPLIPEGDWFCRKC 46

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  269 CVLCPNKGGAFKQTSDG-HWAHVVCAIWIPEVCFANTVFLEPIEGIDNIPPARWKLTCYICKQKgLGAAIQCHKVNCYTA 347
Cdd:cd15704      4 CLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEK-VGASIQCSVKNCRTA 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1511976403  348 FHVTCAQRAGLFMKIEPMRETSlngtiftVRKTAYCEAHS 387
Cdd:cd15704     83 FHVTCAFDRGLEMKTILAENDE-------VKFKSYCPKHS 115

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1511976403  267 VDCVLCPNKGGAFKQTSDGHWAHVVCAIWIPEVCFANTVFLEPIEgIDNIPPARWKLTCYICKQKGL------GAAIQCH 340
Cdd:cd15709      3 VRCELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIV-LQYVPHDRFNKTCYICEEQGReskaasGACMTCN 81