1S5J,1Q9Y,1D5A,1Q8I,1CLQ,1Q9X


Conserved Protein Domain Family
POLBc

?
cd00145: POLBc 
Click on image for an interactive view with Cn3D
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Statistics
?
PSSM-Id: 99912
View PSSM: cd00145
Aligned: 17 rows
Threshold Bit Score: 239.579
Threshold Setting Gi: 118841
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
?
Program:
Drawing:
Aligned Rows:
 
active sitemetal-binding
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1Q9Y; Bacteriophage RB69 POLBc binds 8-oxodG:dCTP
    View structure with Cn3D
  • Comment:Based on similarity to bacteriophage RB69 POLBc (1Q9Y)

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                             #  ###                                                   
1S5J_A     457 KGYKGAVVIDp-pAGIFFNITVLDFASLYPSIIRTWNLSYETVdiqqckkpyevkde----------------------- 512  Sulfolobus solfa...
O60673    2591 APQCVPLIMEpesRFYSNSVLVLDFQSLYPSIVIAYNYCFSTClghvenlgkydefkfgctslrvppdllyqvrhditvs 2670 human
NP_111564  272 KRDRGGLVFQp-vPGIYRDVYEIDFSSMYPSIIVKYNLSPGNVkflpe-------------------------------- 318  Thermoplasma vol...
1Q9Y_A     392 QPYPGAFVKEp-iPNRYKYVMSFDLTSLYPSIIRQVNISPETIagtfkvaplhdyinavaerp------------sdvys 458  Enterobacteria p...
P90829     551 EGYEGATVIDpirGFYNEPIATLDFASLYPSIMIAHNLCYTTLlkspqgvenedyirt---------------------- 608  Caenorhabditis e...
YP_386125  389 GTFEGGYAAVf-eTGVLGPIVHCDVASLYPSIMLAYGLDPRREhl----------------------------------- 432  Unknown
1D5A_A     382 ESYAGGYVKEp-eKGLWENIVYLDYKSLYPSIIITHNVSPDTLnregcreydvap------------------------- 435  Desulfurococcus ...
P26019     857 AAYAGGLVLEpmrGLYEKYVLLMDFNSLYPSIIQEYNICFTTVqqpvdadelp--------------------------- 909  fruit fly
1Q8I_A     397 HASPGGYVMDs-rPGLYDSVLVLDYKSLYPSIVRTFLIDPVGLvegmaqpdpehst------------------------ 451  Escherichia coli
1CLQ_A     389 QPYPGAFVKEp-iPNRYKYVMSFDLTSLYPSIIRQVNISPETIagtfkvaplhdyinavaerp------------sdvys 455  Bacteriophage RB69
Feature 1                                #                                                     
1S5J_A     513 tgevlhivcmdrpgITAVITGLLRDFRVkiykkkaknpnn---------------------------------------- 552  Sulfolobus solfa...
O60673    2671 pngvafvkpsvrkgVLPRMLEEILKTRFmvkqsmkaykq----------------------------------------- 2709 human
NP_111564  319 ----------alngLLERRLFYKRISASsevy------------------------------------------------ 340  Thermoplasma vol...
1Q9Y_A     459 cspngmmyykdrdgVVPTEITKVFNQRKehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsa 538  Enterobacteria p...
P90829     609 psgqyfatkskrrgLLPEILEDILAARKrakndmknekd----------------------------------------- 647  Caenorhabditis e...
YP_386125  433 -------------gLFLPLLAQLRQFRLaakerareaal----------------------------------------- 458  Unknown
1D5A_A     436 --qvghrfckdfpgFIPSLLGDLLEERQkvkkkmkatvd----------------------------------------- 472  Desulfurococcus ...
P26019     910 ----tlpdsktepgILPLQLKRLVESRKevkklmaapdl----------------------------------------- 944  fruit fly
1Q8I_A     452 -egfldawfsrekhCLPEIVTNIWHGRDeakrq----------------------------------------------- 483  Escherichia coli
1CLQ_A     456 cspngmmyykdrdgVVPTEITKVFNQRKehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsa 535  Bacteriophage RB69
Feature 1                              #   #                                                   
1S5J_A     553 ---------seeqkllydvvQRAMKVFINATYGVFGAEtf-plYAPRVAESVTALGRYVITSTVKKARee---------- 612  Sulfolobus solfa...
O60673    2710 ---------dralsrmldarQLGLKLIANVTFGYTSANfsgrmPCIEVGDSIVHKARETLERAIKLVNdtkk-------- 2772 human
NP_111564  341 -----------------snrNAALKWLLLTSFGYTGYKna-kfGKIEVHEDITEIGRKLLADAISIAHdh---------- 392  Thermoplasma vol...
1Q9Y_A     539 kslnemlfraqrtevagmtaQINRKLLINSLYGALGNVwf-ryYDLRNATAITTFGQMALQWIERKVNeylnevc---gt 614  Enterobacteria p...
P90829     648 ----------efkrmvyngrQLALKISANSVYGFTGATvg-klPCLEISQSVTAFGRKMIDMTKLEVEriykkgaldgkc 716  Caenorhabditis e...
YP_386125  459 ----------pherdyfnalQQTFKVLINSFYGYLGTTih-tfSDPGVAAEVTRRGRELIQDMIEWLRrh---------- 517  Unknown
1D5A_A     473 ----------pierklldyrQRAIKILANSYYGYYAYAna-rwYCRECAESVTAWGRQYIETTMREIEekf--------- 532  Desulfurococcus ...
P26019     945 ---------spelqmqyhirQMALKLTANSMYGCLGFAhs-rfFAQHLAALVTHKGREILTNTQQLVQkm---------- 1004 fruit fly
1Q8I_A     484 ---------------gnkplSQALKIIMNAFYGVLGTTac-rfFDPRLASSITMRGHQIMRQTKALIEaq---------- 537  Escherichia coli
1CLQ_A     536 kslnemlfraqrtevagmtaQINRKLLINSLYGALGNVwf-ryYDLRNATAITTFGQMALQWIERKVNeylnevc---gt 611  Bacteriophage RB69
Feature 1                 #                                                                    
1S5J_A     613 --glTVLYGDTDSLFLLnpp-------------------------knsLENIIKWVKTtf---------nLDLEVDKty- 655  Sulfolobus solfa...
O60673    2773 -wgaRVVYGDTDSMFVLlkg--------------------------atKEQSFKIGQEiaeavtatnpkpVKLKFEKvy- 2824 human
NP_111564  393 --gfEMIHGIVDSLWISgn---------------------------gdIEEVIREIRErtmv----divvSGHYRWIvf- 438  Thermoplasma vol...
1Q9Y_A     615 egeaFVLYGDTDSIYVSadkiidkvgeskfrdtnhwvdfldkfarermEPAIDRGFREmceymn-nkqhlMFMDREAiag 693  Enterobacteria p...
P90829     717 padaKVIYGDTDSVMVKfgvetv-------------------aqameiGLDAAKEVSKift-------ppIKLEFEKvy- 769  Caenorhabditis e...
YP_386125  518 --gaRPVEVDTDGIYFIppqgi---------------------etigqEEALVRELSAtlp-------egIAVEMDGry- 566  Unknown
1D5A_A     533 --gfKVLYADTDGFFATipgadae------------------tvknkaKEFLNYINPRlp--------glLELEYEGfy- 583  Desulfurococcus ...
P26019    1005 --nyDVVYGDTDSLMINtni--------------------------tdYDQVYKIGHNikqsvn-klykqLELDIDGvf- 1054 fruit fly
1Q8I_A     538 --gyDVIYGDTDSTFVWlkgahseee--------------aakigralVQHVNAWWAEtlqkq--rltsaLELEYEThf- 598  Escherichia coli
1CLQ_A     612 egeaFVLYGDTDSIYVSadkiidkvgeskfrdtnhwvdfldkfarermEPAIDRGFREmceymn-nkqhlMFMDREAiag 690  Bacteriophage RB69
Feature 1                                                                                      
1S5J_A     656 -------kFVAFsg-------lKKNYFGVyq--------dGKVDIKGmlVKKRntpEFVKKVFNEVKELmisinspndvk 713  Sulfolobus solfa...
O60673    2825 -------lPCVLq--------tKKRYVGYmyetl--dqkdPVFDAKGieTVRRdscPAVSKILERSLKLlfetrd----- 2882 human
NP_111564  439 -------lPENDgs------gsPSRYYGLdy--------nGSYKVRGieLRRAdapEICKRFQVEALEVlre-------- 489  Thermoplasma vol...
1Q9Y_A     694 pplgskgiGGFWt--------gKKRYALNvwdmegtryaePKLKIMGleTQKSstpKAVQKALKECIRRmlqeg------ 759  Enterobacteria p...
P90829     770 -------sPYLLi--------nKKRYAGLyftk---pdvhDKMDCKGleTVRRdncPLVAKVLGVCLEKllier------ 825  Caenorhabditis e...
YP_386125  567 -------rAIFSy--------kIKNYALLdh--------dGKVIVRGsaLRSRgieRYLRDFMAAAVRLllqgd------ 617  Unknown
1D5A_A     584 -------rRGFFv--------tKKKYAVIde--------eDKITTRGleIVRRdwsEIAKETQARVLEAilkhg------ 634  Desulfurococcus ...
P26019    1055 -------gCLLLl--------kKKKYAAIklskdskgnlrREQEHKGldIVRRdwsQLAVMVGKAVLDEvlsek------ 1113 fruit fly
1Q8I_A     599 -------cRFLMptirgadtgsKKRYAGLiqe-----gdkQRMVFKGleTVRTdwtPLAQQFQQELYLRifrn------- 659  Escherichia coli
1CLQ_A     691 pplgskgiGGFWt--------gKKRYALNvwdmegtryaePKLKIMGleTQKSstpKAVQKALKECIRRmlqeg------ 756  Bacteriophage RB69
Feature 1                                                                                      
1S5J_A     714 eikrkIVDVVKGSYEKlknkgynldelafkvmlskplday--------kkntpqhvkaalqlrpfgvnvlprDIIYYVKv 785  Sulfolobus solfa...
O60673    2883 islikQYVQRQCMKLLegkasiqdfifakeyrgsfsykpg--------acvpaleltrkmltydrrsepqvgERVPYVIi 2954 human
NP_111564  490 --crtVEDVMSSKAKIealehryiknirrfplnyftiskkitr--hsseysvntvtrsalkaaetfgkvslgQIIKYTVs 565  Thermoplasma vol...
1Q9Y_A     760 -eeslQEYFKEFEKEFrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegEKVYVLPl 838  Enterobacteria p...
P90829     826 dqqsaLDFAKRTISDLlcnkidislliiskeltksgdkyq--------akqahvelaarmkkrdagsaprlgDRVPYVFv 897  Caenorhabditis e...
YP_386125  618 -gakiPAFHEDCIRRLrnhlipieslartetlgeapptylqk-----vrqgkrnpsaafeialraerpfragDQISYYVt 691  Unknown
1D5A_A     635 dveeaVRIVKEVTEKLsrhevppeklvi---------------------------------yeagphvaaaaTVISYIVl 681  Desulfurococcus ...
P26019    1114 pleekLDAVHAQLEKIktqiaegvvplplfvitkqltrtpqey---ansaslphvqvalrmnrernrrykkgDMVDYVIc 1190 fruit fly
1Q8I_A     660 --epyQEYVRETIDKLmageldarlvyrkrlrr----------------------plseyqrnvpphvraarLADEENQk 715  Escherichia coli
1CLQ_A     757 -eeslQEYFKEFEKEFrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegEKVYVLPl 835  Bacteriophage RB69
Feature 1                                                         
1S5J_A     786 rskdgvkp---------------vqlakvteiDAEKYLEa-lRSTFEQILR 820  Sulfolobus solfataricus
O60673    2955 ygtpgvpliqlvr------rpvevlqdptlrlNATYYITkqiLPPLARIFS 2999 human
NP_111564  566 desrkiv-----------------nldddgtiDYRYYERclrRAFQPFDFI 599  Thermoplasma volcanium GSS1
1Q9Y_A     839 regnpfgdkciawps-gteitdlikddvlhwmDYTVLLEktfIKPLEGFTS 888  Enterobacteria phage RB69
P90829     898 aaaknvpayera-------edptfvlqnniplDTKHYLTnqlAKPLARIFE 941  Caenorhabditis elegans
YP_386125  692 ghgkgvtvyenc-------kpvsqydptrpdeNTEFYLDklnQLVKRLAAY 735  Unknown
1D5A_A     682 kgpgrvgdrai---------pfdefdpakhryDAEYYIEnqvLPAVERILR 723  Desulfurococcus sp. Tok
P26019    1191 ldgttnaamqrayh----ldelktsedkklqlDTNYYLGhqiHPVVTRMVE 1237 fruit fly
1Q8I_A     716 rgrplqyqnrgtikyvwttngpepldyqrsplDYEHYLTrqlQPVAEGILP 766  Escherichia coli
1CLQ_A     836 regnpfgdkciawps-gteitdlikddvlhwmDYTVLLEktfIKPLEGFTS 885  Bacteriophage RB69

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap