Conserved Protein Domain Family
POLBc

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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
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PSSM-Id: 99912
View PSSM: cd00145
Aligned: 17 rows
Threshold Bit Score: 239.579
Threshold Setting Gi: 118841
Created: 1-Nov-2000
Updated: 17-Jan-2013
Structure
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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
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                #  ###                                                   
1S5J_A        457 KGYKGAVVIDp-pAGIFFNITVLDFASLYPSIIRTWNLSYETVdiqqckkpyevkde----------------------- 512
gi 143811385 2591 APQCVPLIMEpesRFYSNSVLVLDFQSLYPSIVIAYNYCFSTClghvenlgkydefkfgctslrvppdllyqvrhditvs 2670
gi 13541876   272 KRDRGGLVFQp-vPGIYRDVYEIDFSSMYPSIIVKYNLSPGNVkflpe-------------------------------- 318
1Q9Y_A        392 QPYPGAFVKEp-iPNRYKYVMSFDLTSLYPSIIRQVNISPETIagtfkvaplhdyinavaerp------------sdvys 458
gi 13124199   551 EGYEGATVIDpirGFYNEPIATLDFASLYPSIMIAHNLCYTTLlkspqgvenedyirt---------------------- 608
gi 78224378   389 GTFEGGYAAVf-eTGVLGPIVHCDVASLYPSIMLAYGLDPRREhl----------------------------------- 432
1D5A_A        382 ESYAGGYVKEp-eKGLWENIVYLDYKSLYPSIIITHNVSPDTLnregcreydvap------------------------- 435
gi 45644974   857 AAYAGGLVLEpmrGLYEKYVLLMDFNSLYPSIIQEYNICFTTVqqpvdadelp--------------------------- 909
1Q8I_A        397 HASPGGYVMDs-rPGLYDSVLVLDYKSLYPSIVRTFLIDPVGLvegmaqpdpehst------------------------ 451
1CLQ_A        389 QPYPGAFVKEp-iPNRYKYVMSFDLTSLYPSIIRQVNISPETIagtfkvaplhdyinavaerp------------sdvys 455
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                   #                                                     
1S5J_A        513 tgevlhivcmdrpgITAVITGLLRDFRVkiykkkaknpnn---------------------------------------- 552
gi 143811385 2671 pngvafvkpsvrkgVLPRMLEEILKTRFmvkqsmkaykq----------------------------------------- 2709
gi 13541876   319 ----------alngLLERRLFYKRISASsevy------------------------------------------------ 340
1Q9Y_A        459 cspngmmyykdrdgVVPTEITKVFNQRKehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsa 538
gi 13124199   609 psgqyfatkskrrgLLPEILEDILAARKrakndmknekd----------------------------------------- 647
gi 78224378   433 -------------gLFLPLLAQLRQFRLaakerareaal----------------------------------------- 458
1D5A_A        436 --qvghrfckdfpgFIPSLLGDLLEERQkvkkkmkatvd----------------------------------------- 472
gi 45644974   910 ----tlpdsktepgILPLQLKRLVESRKevkklmaapdl----------------------------------------- 944
1Q8I_A        452 -egfldawfsrekhCLPEIVTNIWHGRDeakrq----------------------------------------------- 483
1CLQ_A        456 cspngmmyykdrdgVVPTEITKVFNQRKehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsa 535
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                 #   #                                                   
1S5J_A        553 ---------seeqkllydvvQRAMKVFINATYGVFGAEtf-plYAPRVAESVTALGRYVITSTVKKARee---------- 612
gi 143811385 2710 ---------dralsrmldarQLGLKLIANVTFGYTSANfsgrmPCIEVGDSIVHKARETLERAIKLVNdtkk-------- 2772
gi 13541876   341 -----------------snrNAALKWLLLTSFGYTGYKna-kfGKIEVHEDITEIGRKLLADAISIAHdh---------- 392
1Q9Y_A        539 kslnemlfraqrtevagmtaQINRKLLINSLYGALGNVwf-ryYDLRNATAITTFGQMALQWIERKVNeylnevc---gt 614
gi 13124199   648 ----------efkrmvyngrQLALKISANSVYGFTGATvg-klPCLEISQSVTAFGRKMIDMTKLEVEriykkgaldgkc 716
gi 78224378   459 ----------pherdyfnalQQTFKVLINSFYGYLGTTih-tfSDPGVAAEVTRRGRELIQDMIEWLRrh---------- 517
1D5A_A        473 ----------pierklldyrQRAIKILANSYYGYYAYAna-rwYCRECAESVTAWGRQYIETTMREIEekf--------- 532
gi 45644974   945 ---------spelqmqyhirQMALKLTANSMYGCLGFAhs-rfFAQHLAALVTHKGREILTNTQQLVQkm---------- 1004
1Q8I_A        484 ---------------gnkplSQALKIIMNAFYGVLGTTac-rfFDPRLASSITMRGHQIMRQTKALIEaq---------- 537
1CLQ_A        536 kslnemlfraqrtevagmtaQINRKLLINSLYGALGNVwf-ryYDLRNATAITTFGQMALQWIERKVNeylnevc---gt 611
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #                                                                    
1S5J_A        613 --glTVLYGDTDSLFLLnpp-------------------------knsLENIIKWVKTtf---------nLDLEVDKty- 655
gi 143811385 2773 -wgaRVVYGDTDSMFVLlkg--------------------------atKEQSFKIGQEiaeavtatnpkpVKLKFEKvy- 2824
gi 13541876   393 --gfEMIHGIVDSLWISgn---------------------------gdIEEVIREIRErtmv----divvSGHYRWIvf- 438
1Q9Y_A        615 egeaFVLYGDTDSIYVSadkiidkvgeskfrdtnhwvdfldkfarermEPAIDRGFREmceymn-nkqhlMFMDREAiag 693
gi 13124199   717 padaKVIYGDTDSVMVKfgvetv-------------------aqameiGLDAAKEVSKift-------ppIKLEFEKvy- 769
gi 78224378   518 --gaRPVEVDTDGIYFIppqgi---------------------etigqEEALVRELSAtlp-------egIAVEMDGry- 566
1D5A_A        533 --gfKVLYADTDGFFATipgadae------------------tvknkaKEFLNYINPRlp--------glLELEYEGfy- 583
gi 45644974  1005 --nyDVVYGDTDSLMINtni--------------------------tdYDQVYKIGHNikqsvn-klykqLELDIDGvf- 1054
1Q8I_A        538 --gyDVIYGDTDSTFVWlkgahseee--------------aakigralVQHVNAWWAEtlqkq--rltsaLELEYEThf- 598
1CLQ_A        612 egeaFVLYGDTDSIYVSadkiidkvgeskfrdtnhwvdfldkfarermEPAIDRGFREmceymn-nkqhlMFMDREAiag 690
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1S5J_A        656 -------kFVAFsg-------lKKNYFGVyq--------dGKVDIKGmlVKKRntpEFVKKVFNEVKELmisinspndvk 713
gi 143811385 2825 -------lPCVLq--------tKKRYVGYmyetl--dqkdPVFDAKGieTVRRdscPAVSKILERSLKLlfetrd----- 2882
gi 13541876   439 -------lPENDgs------gsPSRYYGLdy--------nGSYKVRGieLRRAdapEICKRFQVEALEVlre-------- 489
1Q9Y_A        694 pplgskgiGGFWt--------gKKRYALNvwdmegtryaePKLKIMGleTQKSstpKAVQKALKECIRRmlqeg------ 759
gi 13124199   770 -------sPYLLi--------nKKRYAGLyftk---pdvhDKMDCKGleTVRRdncPLVAKVLGVCLEKllier------ 825
gi 78224378   567 -------rAIFSy--------kIKNYALLdh--------dGKVIVRGsaLRSRgieRYLRDFMAAAVRLllqgd------ 617
1D5A_A        584 -------rRGFFv--------tKKKYAVIde--------eDKITTRGleIVRRdwsEIAKETQARVLEAilkhg------ 634
gi 45644974  1055 -------gCLLLl--------kKKKYAAIklskdskgnlrREQEHKGldIVRRdwsQLAVMVGKAVLDEvlsek------ 1113
1Q8I_A        599 -------cRFLMptirgadtgsKKRYAGLiqe-----gdkQRMVFKGleTVRTdwtPLAQQFQQELYLRifrn------- 659
1CLQ_A        691 pplgskgiGGFWt--------gKKRYALNvwdmegtryaePKLKIMGleTQKSstpKAVQKALKECIRRmlqeg------ 756
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1S5J_A        714 eikrkIVDVVKGSYEKlknkgynldelafkvmlskplday--------kkntpqhvkaalqlrpfgvnvlprDIIYYVKv 785
gi 143811385 2883 islikQYVQRQCMKLLegkasiqdfifakeyrgsfsykpg--------acvpaleltrkmltydrrsepqvgERVPYVIi 2954
gi 13541876   490 --crtVEDVMSSKAKIealehryiknirrfplnyftiskkitr--hsseysvntvtrsalkaaetfgkvslgQIIKYTVs 565
1Q9Y_A        760 -eeslQEYFKEFEKEFrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegEKVYVLPl 838
gi 13124199   826 dqqsaLDFAKRTISDLlcnkidislliiskeltksgdkyq--------akqahvelaarmkkrdagsaprlgDRVPYVFv 897
gi 78224378   618 -gakiPAFHEDCIRRLrnhlipieslartetlgeapptylqk-----vrqgkrnpsaafeialraerpfragDQISYYVt 691
1D5A_A        635 dveeaVRIVKEVTEKLsrhevppeklvi---------------------------------yeagphvaaaaTVISYIVl 681
gi 45644974  1114 pleekLDAVHAQLEKIktqiaegvvplplfvitkqltrtpqey---ansaslphvqvalrmnrernrrykkgDMVDYVIc 1190
1Q8I_A        660 --epyQEYVRETIDKLmageldarlvyrkrlrr----------------------plseyqrnvpphvraarLADEENQk 715
1CLQ_A        757 -eeslQEYFKEFEKEFrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegEKVYVLPl 835
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|.
Feature 1                                                            
1S5J_A        786 rskdgvkp---------------vqlakvteiDAEKYLEa-lRSTFEQILR 820
gi 143811385 2955 ygtpgvpliqlvr------rpvevlqdptlrlNATYYITkqiLPPLARIFS 2999
gi 13541876   566 desrkiv-----------------nldddgtiDYRYYERclrRAFQPFDFI 599
1Q9Y_A        839 regnpfgdkciawps-gteitdlikddvlhwmDYTVLLEktfIKPLEGFTS 888
gi 13124199   898 aaaknvpayera-------edptfvlqnniplDTKHYLTnqlAKPLARIFE 941
gi 78224378   692 ghgkgvtvyenc-------kpvsqydptrpdeNTEFYLDklnQLVKRLAAY 735
1D5A_A        682 kgpgrvgdrai---------pfdefdpakhryDAEYYIEnqvLPAVERILR 723
gi 45644974  1191 ldgttnaamqrayh----ldelktsedkklqlDTNYYLGhqiHPVVTRMVE 1237
1Q8I_A        716 rgrplqyqnrgtikyvwttngpepldyqrsplDYEHYLTrqlQPVAEGILP 766
1CLQ_A        836 regnpfgdkciawps-gteitdlikddvlhwmDYTVLLEktfIKPLEGFTS 885

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