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Conserved domains on  [gi|767967784|ref|XP_011543179|]
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DNA polymerase alpha subunit B isoform X1 [Homo sapiens]

Protein Classification

Pol_alpha_B_N and DNA_pol_E_B domain-containing protein( domain architecture ID 13566362)

Pol_alpha_B_N and DNA_pol_E_B domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 342-549 1.81e-66

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


:

Pssm-ID: 461142  Cd Length: 210  Bit Score: 215.64  E-value: 1.81e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  342 VLVACGPYTTSDSITYDPLLDLIAVINHD-RPDVCILFGPFLDAKHEQVENCLL---TSPFEDIFKQCLRTIIEGTRSSg 417
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNEDsPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQLLEK- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  418 SHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKK-QVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFS 496
Cdd:pfam04042  80 TPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFL 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767967784  497 RILKHILTQRSYYPLYPPqEDMAIDYESFYVYAqLPVTPDVLIIPSELRYFVK 549
Cdd:pfam04042 160 RLVETILRQRHLAPLAPD-TLRPYPYDKDDAFV-LYPLPDVLILGSELPSFAK 210
Pol_alpha_B_N super family cl37775
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 111-238 1.82e-07

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


The actual alignment was detected with superfamily member pfam08418:

Pssm-ID: 462470  Cd Length: 240  Bit Score: 52.33  E-value: 1.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  111 NSYTTPSKGSQKRAI--------STPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQkYNSRSNRGEVVTSFG----LAQ 178
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNphleLAE 173

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  179 GVSwSGRGGAgNISLKVLGCPEALtgSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIE 238
Cdd:pfam08418 174 PPI-APYSEP-RVKLTANTDPKKY--KYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
 
Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 342-549 1.81e-66

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 215.64  E-value: 1.81e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  342 VLVACGPYTTSDSITYDPLLDLIAVINHD-RPDVCILFGPFLDAKHEQVENCLL---TSPFEDIFKQCLRTIIEGTRSSg 417
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNEDsPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQLLEK- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  418 SHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKK-QVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFS 496
Cdd:pfam04042  80 TPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFL 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767967784  497 RILKHILTQRSYYPLYPPqEDMAIDYESFYVYAqLPVTPDVLIIPSELRYFVK 549
Cdd:pfam04042 160 RLVETILRQRHLAPLAPD-TLRPYPYDKDDAFV-LYPLPDVLILGSELPSFAK 210
POL12 COG5214
DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, ...
 206-549 7.25e-61

DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair];


Pssm-ID: 227539 [Multi-domain]  Cd Length: 581  Bit Score: 211.76  E-value: 7.25e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 206 YKSMFQKLPDIREVLTCKIEELGSELKEHYKI--EAFTPLLAPAQEPVTLLGQIGCDS---NGKLNNKSVILEGDREHSS 280
Cdd:COG5214  158 SRFMYQKLRKKSKVLDDRIELFSMKPYFLYLLsiEDFAPPNNVSQSSFYTVGRIVNPStnfGHKLNSESVFLESSRDGGN 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 281 GAQIPVDLSELKEYSLFPGQVVIMEGINTTGRKLVATKLYegvPLPFY-----QPTEEDADFEQSM------VLVACGPY 349
Cdd:COG5214  238 GVRVRLNLAHLQRYSVFPGQIVAVKGKNTDGGKFTVEAIL---PIPVVpinpaSDGQEKKYFQANTnnqptsIVAFSGPY 314

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 350 TTSDSITYDPLLDLIAVINHDRPDVCILFGPFLDAKHEQVENCLLTSP----FEDIFKQCLRTIIEgtRSSGSHLVFVPS 425
Cdd:COG5214  315 GPRDDLSGSPLFDAIDRVNANDVDVLILIGPFIDINHILIQYGATQSTpdsmLKELFIPRITPILD--RNAGPKAVLIPS 392

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 426 LRD-VHHEPVYPQPPFSYSDLSRedKKQVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTS--DRFSRILKHI 502
Cdd:COG5214  393 TNDaTSCHNAFPQGPIGRNALRL--PSNFKCTGNPCEFFINEILFGISSLDTPLEISSEECFHDSLLSggDRLGRISYHL 470

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767967784 503 LTQRSYYPLYPPQEDMAIDYESFYV-YAQLP-----VTPDVLIIPSELRYFVK 549
Cdd:COG5214  471 LFQRTFYPVFPGGSLEKCNPSSLDVvSLSLPefmsmTAPDIYIVPSKLKHFCR 523
Pol_alpha_B_N pfam08418
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 111-238 1.82e-07

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


Pssm-ID: 462470  Cd Length: 240  Bit Score: 52.33  E-value: 1.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  111 NSYTTPSKGSQKRAI--------STPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQkYNSRSNRGEVVTSFG----LAQ 178
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNphleLAE 173

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  179 GVSwSGRGGAgNISLKVLGCPEALtgSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIE 238
Cdd:pfam08418 174 PPI-APYSEP-RVKLTANTDPKKY--KYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 407-539 3.93e-05

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277332  Cd Length: 243  Bit Score: 45.37  E-value: 3.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 407 RTIIEGTRSSGSHLVFVPSlrDVH-------HEPVY---PQPPFSYSDLSREDKKQVQFVSEPCSLSINGVIFgltstdL 476
Cdd:cd07386   62 LDIYEQYEEAAEYLSDVPS--HIKiiiipgnHDAVRqaePQPALPEEIRKLFYPGNVEFLSNPALVKIHGVDV------L 133

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767967784 477 LFHlGA---EEISSSSGTS-DRFSRILKHILTQRSYYPLYPPQEDMAIDYESFYVYAQLpvtPDVLI 539
Cdd:cd07386  134 IYH-GRsldDVVGLIPGLSyDKPGKAMEELLKRRHLAPIYGGRTPIAPEAEDYLVIDEV---PDILH 196
 
Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 342-549 1.81e-66

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 215.64  E-value: 1.81e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  342 VLVACGPYTTSDSITYDPLLDLIAVINHD-RPDVCILFGPFLDAKHEQVENCLL---TSPFEDIFKQCLRTIIEGTRSSg 417
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNEDsPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQLLEK- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  418 SHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKK-QVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFS 496
Cdd:pfam04042  80 TPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFL 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767967784  497 RILKHILTQRSYYPLYPPqEDMAIDYESFYVYAqLPVTPDVLIIPSELRYFVK 549
Cdd:pfam04042 160 RLVETILRQRHLAPLAPD-TLRPYPYDKDDAFV-LYPLPDVLILGSELPSFAK 210
POL12 COG5214
DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, ...
 206-549 7.25e-61

DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair];


Pssm-ID: 227539 [Multi-domain]  Cd Length: 581  Bit Score: 211.76  E-value: 7.25e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 206 YKSMFQKLPDIREVLTCKIEELGSELKEHYKI--EAFTPLLAPAQEPVTLLGQIGCDS---NGKLNNKSVILEGDREHSS 280
Cdd:COG5214  158 SRFMYQKLRKKSKVLDDRIELFSMKPYFLYLLsiEDFAPPNNVSQSSFYTVGRIVNPStnfGHKLNSESVFLESSRDGGN 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 281 GAQIPVDLSELKEYSLFPGQVVIMEGINTTGRKLVATKLYegvPLPFY-----QPTEEDADFEQSM------VLVACGPY 349
Cdd:COG5214  238 GVRVRLNLAHLQRYSVFPGQIVAVKGKNTDGGKFTVEAIL---PIPVVpinpaSDGQEKKYFQANTnnqptsIVAFSGPY 314

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 350 TTSDSITYDPLLDLIAVINHDRPDVCILFGPFLDAKHEQVENCLLTSP----FEDIFKQCLRTIIEgtRSSGSHLVFVPS 425
Cdd:COG5214  315 GPRDDLSGSPLFDAIDRVNANDVDVLILIGPFIDINHILIQYGATQSTpdsmLKELFIPRITPILD--RNAGPKAVLIPS 392

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 426 LRD-VHHEPVYPQPPFSYSDLSRedKKQVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTS--DRFSRILKHI 502
Cdd:COG5214  393 TNDaTSCHNAFPQGPIGRNALRL--PSNFKCTGNPCEFFINEILFGISSLDTPLEISSEECFHDSLLSggDRLGRISYHL 470

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767967784 503 LTQRSYYPLYPPQEDMAIDYESFYV-YAQLP-----VTPDVLIIPSELRYFVK 549
Cdd:COG5214  471 LFQRTFYPVFPGGSLEKCNPSSLDVvSLSLPefmsmTAPDIYIVPSKLKHFCR 523
Pol_alpha_B_N pfam08418
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 111-238 1.82e-07

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


Pssm-ID: 462470  Cd Length: 240  Bit Score: 52.33  E-value: 1.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  111 NSYTTPSKGSQKRAI--------STPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQkYNSRSNRGEVVTSFG----LAQ 178
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNphleLAE 173

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784  179 GVSwSGRGGAgNISLKVLGCPEALtgSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIE 238
Cdd:pfam08418 174 PPI-APYSEP-RVKLTANTDPKKY--KYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 407-539 3.93e-05

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277332  Cd Length: 243  Bit Score: 45.37  E-value: 3.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767967784 407 RTIIEGTRSSGSHLVFVPSlrDVH-------HEPVY---PQPPFSYSDLSREDKKQVQFVSEPCSLSINGVIFgltstdL 476
Cdd:cd07386   62 LDIYEQYEEAAEYLSDVPS--HIKiiiipgnHDAVRqaePQPALPEEIRKLFYPGNVEFLSNPALVKIHGVDV------L 133

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767967784 477 LFHlGA---EEISSSSGTS-DRFSRILKHILTQRSYYPLYPPQEDMAIDYESFYVYAQLpvtPDVLI 539
Cdd:cd07386  134 IYH-GRsldDVVGLIPGLSyDKPGKAMEELLKRRHLAPIYGGRTPIAPEAEDYLVIDEV---PDILH 196
 
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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