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Conserved domains on  [gi|224586804|ref|NP_059139|]
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DNA polymerase epsilon subunit 3 [Homo sapiens]

Protein Classification

histone H3/H4 domain-containing protein( domain architecture ID 581047)

histone H3/H4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 6-92 1.24e-43

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


:

Pssm-ID: 467053  Cd Length: 87  Bit Score: 138.41  E-value: 1.24e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   6 EDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPL 85
Cdd:cd22928    1 DDLELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPL 80


                 ....*..
gi 224586804  86 KEALEAY 92
Cdd:cd22928   81 KEELEAY 87
 
Name Accession Description Interval E-value
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 6-92 1.24e-43

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 138.41  E-value: 1.24e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   6 EDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPL 85
Cdd:cd22928    1 DDLELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPL 80


                 ....*..
gi 224586804  86 KEALEAY 92
Cdd:cd22928   81 KEELEAY 87
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
1-105 4.22e-10

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 54.59  E-value: 4.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   1 MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQR 80
Cdd:COG5150    3 MEKNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEE 82

                         90       100
                 ....*....|....*....|....*
gi 224586804  81 FVTPLKEALEAYRREQKGKKEASEQ 105
Cdd:COG5150   83 YIESCMEEHENYKSYQKQKESKISK 107
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 10-73 4.10e-08

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 47.22  E-value: 4.10e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 224586804   10 LPNAVITRIIKEAlPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAM 73
Cdd:pfam00808   3 LPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
 
Name Accession Description Interval E-value
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 6-92 1.24e-43

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 138.41  E-value: 1.24e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   6 EDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPL 85
Cdd:cd22928    1 DDLELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPL 80


                 ....*..
gi 224586804  86 KEALEAY 92
Cdd:cd22928   81 KEELEAY 87
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 3-93 1.50e-21

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


Pssm-ID: 467032  Cd Length: 91  Bit Score: 82.60  E-value: 1.50e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   3 ERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFV 82
Cdd:cd22907    1 LREQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYV 80

                         90
                 ....*....|.
gi 224586804  83 TPLKEALEAYR 93
Cdd:cd22907   81 EPLKIYLQKYR 91
HFD_Dr1 cd22905
histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator ...
 6-103 3.45e-18

histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4.


Pssm-ID: 467030  Cd Length: 129  Bit Score: 74.91  E-value: 3.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   6 EDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPL 85
Cdd:cd22905    2 DDLSLPKATVNKLIKEVLPPDMRVSKDTRELILECCTEFIHLISSEANEICEKEKKKTISPEHVLKALENLGFGEYIEEV 81

                         90
                 ....*....|....*...
gi 224586804  86 KEALEAYRREQKGKKEAS 103
Cdd:cd22905   82 EEALEDHKEEAKKRPKKS 99
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
1-105 4.22e-10

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 54.59  E-value: 4.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   1 MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQR 80
Cdd:COG5150    3 MEKNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEE 82

                         90       100
                 ....*....|....*....|....*
gi 224586804  81 FVTPLKEALEAYRREQKGKKEASEQ 105
Cdd:COG5150   83 YIESCMEEHENYKSYQKQKESKISK 107
HFD_Dpb3-like cd23645
histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) ...
 10-85 1.93e-08

histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) and similar proteins; Schizosaccharomyces pombe Dpb3 is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that is a heterotetramer consisting of cdc20/Pol2, Dpb2, Dpb3, and Dpb4, and participates in chromosomal DNA replication. Dpb3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. The Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation and H3K9 methylation in heterochromatin. The Dpb3-Dpb4 dimer is also required for the recruitment of sir2 to heterochromatin.


Pssm-ID: 467059 [Multi-domain]  Cd Length: 78  Bit Score: 48.38  E-value: 1.93e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 224586804  10 LPNAVITRIIKEAlPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPL 85
Cdd:cd23645    3 LPLARVKRIIKAD-KDVKICSKDAVFLISKATELFIEYLAEQAYELAKLEKRKTVQYKDLAKAVKRDDNLEFLEDV 77
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 10-73 4.10e-08

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 47.22  E-value: 4.10e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 224586804   10 LPNAVITRIIKEAlPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAM 73
Cdd:pfam00808   3 LPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 8-89 1.35e-07

histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin.


Pssm-ID: 467054 [Multi-domain]  Cd Length: 79  Bit Score: 46.35  E-value: 1.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224586804   8 LNLPNAVITRIIKeALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFvtpLKE 87
Cdd:cd22929    2 PKLPLSRVKRIMK-LDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRFAF---LED 77


                 ..
gi 224586804  88 AL 89
Cdd:cd22929   78 VL 79
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 10-74 1.64e-05

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 40.28  E-value: 1.64e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 224586804  10 LPNAVITRIIKEALPDGvnISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAME 74
Cdd:cd00076    1 LLRSAVARILKSAGFDS--VSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_NFYC-like cd22908
histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar ...
 9-72 3.82e-04

histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins; NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity.


Pssm-ID: 467033 [Multi-domain]  Cd Length: 84  Bit Score: 37.11  E-value: 3.82e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 224586804   9 NLPNAVITRIIKEAlPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSA 72
Cdd:cd22908    7 ELPLARIKKIMKSD-EDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAA 69
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 10-74 4.66e-03

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 33.67  E-value: 4.66e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 224586804  10 LPNAVITRIIKEAlpDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAME 74
Cdd:cd22909    2 LPKAPVKRIIKKA--GAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HAP5 COG5208
CCAAT-binding factor, subunit C [Transcription];
7-82 4.93e-03

CCAAT-binding factor, subunit C [Transcription];


Pssm-ID: 227533 [Multi-domain]  Cd Length: 286  Bit Score: 35.80  E-value: 4.93e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 224586804   7 DLNLPNAVITRIIKeaLPDGVN-ISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFV 82
Cdd:COG5208  107 DHNLPLARIKKVMK--TDEDVKmISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFL 181
 
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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