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Conserved domains on  [gi|281364019|ref|NP_001163253|]
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DNA polymerase epsilon subunit 4, isoform B [Drosophila melanogaster]

Protein Classification

histone-fold protein( domain architecture ID 19224140)

histone-fold protein such as NFYB/HAP3 family histone-like transcription factors similar to transcriptional activator hap3 that belongs to a complex that binds to the sequence CCAAT located upstream of genes involved in mitochondrial electron transport

Gene Ontology:  GO:0046982|GO:0006261|GO:0008622
PubMed:  8524779|17391511

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 75-153 1.91e-33

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: 112.61  E-value: 1.91e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281364019  75 MTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFLDGAM 153
Cdd:cd22929    1 LPKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRFAFLEDVL 79
 
Name Accession Description Interval E-value
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 75-153 1.91e-33

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: 112.61  E-value: 1.91e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281364019  75 MTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFLDGAM 153
Cdd:cd22929    1 LPKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRFAFLEDVL 79
HAP5 COG5208
CCAAT-binding factor, subunit C [Transcription];
65-149 2.95e-13

CCAAT-binding factor, subunit C [Transcription];


Pssm-ID: 227533 [Multi-domain]  Cd Length: 286  Bit Score: 65.46  E-value: 2.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281364019  65 NKAPADNEA--KMTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISA 142
Cdd:COG5208   95 KAAEEERQIllKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK 174


                 ....*..
gi 281364019 143 VDSLLFL 149
Cdd:COG5208  175 SEMFDFL 181
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 78-140 9.36e-13

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: 59.54  E-value: 9.36e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281364019   78 LPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAI 140
Cdd:pfam00808   3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
 
Name Accession Description Interval E-value
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 75-153 1.91e-33

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: 112.61  E-value: 1.91e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281364019  75 MTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFLDGAM 153
Cdd:cd22929    1 LPKLPLSRVKRIMKLDPDVTLVSQEAVVAIAKATELFIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDRFAFLEDVL 79
HFD_NFYC-like cd22908
histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar ...
 74-149 4.31e-23

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: 86.42  E-value: 4.31e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281364019  74 KMTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFL 149
Cdd:cd22908    4 KNHELPLARIKKIMKSDEDVKMISAEAPVLFAKACELFILELTLRAWIHTEENKRRTLQRSDIAAAITSSDMFDFL 79
HFD_Dpb3-like cd23645
histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) ...
 76-150 5.58e-20

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: 78.42  E-value: 5.58e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281364019  76 TQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFLD 150
Cdd:cd23645    1 TVLPLARVKRIIKADKDVKICSKDAVFLISKATELFIEYLAEQAYELAKLEKRKTVQYKDLAKAVKRDDNLEFLE 75
HFD_CHRAC1-like cd22924
histone-fold domain found in chromatin accessibility complex protein 1 (CHRAC-1) and similar ...
 78-149 5.14e-16

histone-fold domain found in chromatin accessibility complex protein 1 (CHRAC-1) and similar proteins; CHRAC-1, also called chromatin accessibility complex 15 kDa protein, or CHRAC-15, or DNA polymerase epsilon subunit p15, forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1. Together with POLE3, ACF1 and ISWI/SNF2H proteins, CHRAC-1 forms the ISWI chromatin-remodeling complex, CHRAC. This subfamily also includes Drosophila melanogaster chromatin accessibility complex 16kD protein (CHRAC-16), which is a histone-like protein that promotes nucleosome sliding of ATP-dependent nucleosome remodeling complexes. It is part of the CHRAC, composed of CHRAC-14, CHRAC-16, ACF and ISWI, which uses energy/ATP to increase the general accessibility of DNA in chromatin. It forms a heterodimer with CHRAC-14, binds DNA, and facilitates nucleosome sliding by ACF. It is required for oogenesis.


Pssm-ID: 467049  Cd Length: 74  Bit Score: 67.97  E-value: 5.14e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 281364019  78 LPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAqsKKKTIQKRDVDMAISAVDSLLFL 149
Cdd:cd22924    1 LPLSRVRTIMKSSPDVSSISQDAVFLITKATELFVEYLAKEAYKKSK--DKKKLTYKDLADVVNDDENLEFL 70
HAP5 COG5208
CCAAT-binding factor, subunit C [Transcription];
65-149 2.95e-13

CCAAT-binding factor, subunit C [Transcription];


Pssm-ID: 227533 [Multi-domain]  Cd Length: 286  Bit Score: 65.46  E-value: 2.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281364019  65 NKAPADNEA--KMTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISA 142
Cdd:COG5208   95 KAAEEERQIllKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK 174


                 ....*..
gi 281364019 143 VDSLLFL 149
Cdd:COG5208  175 SEMFDFL 181
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 78-140 9.36e-13

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: 59.54  E-value: 9.36e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281364019   78 LPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAI 140
Cdd:pfam00808   3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
HFD_DRAP1 cd22906
histone-fold domain found in Dr1-associated protein 1 (DRAP1) and similar proteins; DRAP1, ...
 79-149 1.00e-09

histone-fold domain found in Dr1-associated protein 1 (DRAP1) and similar proteins; DRAP1, also called Dr1-associated corepressor or negative cofactor 2-alpha (NC2-alpha), acts as a corepressor for Dr1 (down-regulator of transcription 1)-mediated repression of transcription. It forms a heterodimer with Dr1. The association of the Dr1/DRAP1 heterodimer with TBP results in a functional repression of both activated and basal transcription of class II genes. DRAP1 can bind to DNA on its own. It also binds TATA-binding protein-associated factor 172 (BTAF1).


Pssm-ID: 467031 [Multi-domain]  Cd Length: 75  Bit Score: 51.75  E-value: 1.00e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281364019  79 PLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAISAVDSLLFL 149
Cdd:cd22906    5 PAARIKKIMQSDEEVGKVAAAVPVLISKALELFLEDLLTKAAEVAKERNAKTITPSHLKQCVESEEKFDFL 75
Histone pfam00125
Core histone H2A/H2B/H3/H4;
77-140 6.09e-08

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 48.58  E-value: 6.09e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281364019   77 QLPLARI-RNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAI 140
Cdd:pfam00125  59 KLPFARVvREVVQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLAR 123
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 78-141 2.33e-06

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: 42.59  E-value: 2.33e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281364019  78 LPLARIRNIMKLDPDlHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAIS 141
Cdd:cd00076    1 LLRSAVARILKSAGF-DSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
BUR6 COG5247
Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription];
60-149 7.30e-06

Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription];


Pssm-ID: 227572  Cd Length: 113  Bit Score: 42.64  E-value: 7.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281364019  60 PVTNGNKAPADNEAK--MTQLPLARIRNIMKLDPDLHMANNEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVD 137
Cdd:COG5247    4 PVGNMGTMPKQNSQKkkKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLK 83

                         90
                 ....*....|..
gi 281364019 138 MAISAVDSLLFL 149
Cdd:COG5247   84 RATESDEKFDFL 95
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 78-141 2.16e-04

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: 37.52  E-value: 2.16e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281364019  78 LPLARIRNIMKLDPDLHMANnEAVFIVAKAVELFIASLSRESYTYTAQSKKKTIQKRDVDMAIS 141
Cdd:cd22909    2 LPKAPVKRIIKKAGAERVSE-DAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
 
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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