1D5A,1QHT,1QQC,1TGO,1WN7,1WNS,2JGU


Conserved Protein Domain Family
POLBc_B3

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cd05536: POLBc_B3 
Click on image for an interactive view with Cn3D
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Statistics
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PSSM-Id: 99919
View PSSM: cd05536
Aligned: 18 rows
Threshold Bit Score: 518.032
Threshold Setting Gi: 495654
Created: 20-Jul-2007
Updated: 2-Oct-2020
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:
  • Comment:Based on similarity to bacteriophage RB69 POLBc (1Q9Y)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                            #  ###                                                   
1D5A_A    381 TESYAGGYVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNRegcreydvapq-----------vghrfckdfpGFI 449 Desulfurococcus sp...
AAA72443  427 KFSYEGGYVREPLKGIQEDIVSLDFMSLYPSILISHNISPETVIYeeker----------------------enmelGII 484 Methanococcus voltae
BAA07580  416 GESYKGAVVLKPLKGVHENVVVLDFSSMYPSIMIKYNVGPDTIVDdpsecpkyggcyv------apevghrfrrsppGFF 489 Pyrodictium occultum
3122019   388 AESYEGAFVLEPERGLHENVACLDFASMYPSIMIAFNISPDTYGCrddcyeapev-------------ghkfrkspdGFF 454 Archaeoglobus fulg...
BAA75663  386 EGRYAGAIVLRPKPGVHEDIAVLDFASMYPNIMVKYNVGPDTLVRpgeeygeeevyta-------pevghkfrksppGFF 458 Aeropyrum pernix
NP_378066 406 YESYEGGLVISPLPGIHEDVYVLDFSSMYPSIMIKYNIGPDTLVKgecencwisp------------aghkfrkdppGLY 473 Sulfolobus tokodaii
NP_614322 428 RKAYKGAIVFEPEIGLHENVVCVDFASLYPNVMVAHNISPDTFDCdccprvtveevddptdatvapdvghkfckrrkGFF 507 Methanopyrus kandl...
YP_254794 407 TEASDEGIIVPPVSGLHNNVYMLDFSTIYPSIILKYNISPDTLVRgdcsdcwtsln-----------gnykfrkdikGLY 475 Sulfolobus acidoca...
YP_919805 412 EETYKGAIVLKPKPGVHKKIAVLDFSSMYPNIMIKYNISPDTYVPpeehvdpsevwva-------pevghrfrkhppGFY 484 Thermofilum penden...
YP_687422 403 VETYAGGFVFEPVKGLHKNVAALDFSAMYPSIMIAYNISPDTVCEagdqdcsepap----------evgyrfkkqpeGFF 472 uncultured methano...
Feature 1               #                              #   #                                  
1D5A_A    450 PSLLGDLLEERQKVKkkmkatvdp----ierklldyrQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTM 525 Desulfurococcus sp...
AAA72443  485 PKTLNELLSRRKHIKmllkdkiqknefdeeysrleheQKSIKVLANSHYGYLAFPMARWYSDKCAEMVTGLGRKYIQETI 564 Methanococcus voltae
BAA07580  490 KTVLENLLKLRRQVKekmkefppds---peyrlyderQKALKVLANASYGYMGWSHARWYCKRCAEAVTAWGRNLILTAI 566 Pyrodictium occultum
3122019   455 KRILRMLIEKRRELKvelknlspes---seyklldikQQTLKVLTNSFYGYMGWNLARWYCHPCAEATTAWGRHFIRTSA 531 Archaeoglobus fulg...
BAA75663  459 KKILERFLSWRRQIRsemkkhppds---peykllderQKAIKLLANASYGYMGWPHARWYCRECAEAVTAWGRSIIRTAI 535 Aeropyrum pernix
NP_378066 474 KNVLEKLIQERKEVKklmektmde----ydkrvldarQRALKVMANAFYGYMGWLGARWYSKEGAEAVTAWGRQIISESA 549 Sulfolobus tokodaii
NP_614322 508 PRLVEGLIERRRELKrrlrkldtesh-pheakildvrQQAYKVLANSYYGYMGWANARWFCRECAESVTAWGRYYISEVR 586 Methanopyrus kandl...
YP_254794 476 QNVLLNLSAEIERREeiiktldpe-----krrrleeeLRALRSILNSFYDYIRWTNARWYVKECAEGLFEWGRELILQIL 550 Sulfolobus acidoca...
YP_919805 485 RKVLESLLEARRRLRekmktldprs---eeyriyderQKAIKVITNATYGYSGWSMARWYKREVAEATTAWGRELIKATI 561 Thermofilum penden...
YP_687422 473 TTILKNLVTHRSTLKkrlaqldrks---neyrmldlrQKSIKILTNAFYGYTGWAQAKWYRRECAEATSAWGRYFIKKAN 549 uncultured methano...
Feature 1                     #                                                               
1D5A_A    526 REIEEKfGFKVLYADTDGFFATIPgadae----------------------tvknkAKEFLNYINPRLPglLELEYEGFY 583 Desulfurococcus sp...
AAA72443  565 EKAEEF-GFKVIYADTDGFYAKWDydklqkgkkeendksdklsnlpklskeeliilTKKFLKGINEELPegMELEFEGHF 643 Methanococcus voltae
BAA07580  567 EYARKL-GLKVIYGDTDSLFVVYDke-----------------------------kVEKLIEFVEKELG--FEIKIDKIY 614 Pyrodictium occultum
3122019   532 KIAESM-GFKVLYGDTDSIFVTKAgmt--------------------------kedVDRLIDKLHEELP--IQIEVDEYY 582 Archaeoglobus fulg...
BAA75663  536 RKAGEL-GLEVIYGDTDSLFVKNDpe-----------------------------kVERLIRFVEEELG--FDIKVDKVY 583 Aeropyrum pernix
NP_378066 550 KIAKEK-GFTVIYGDTDSIFVKGGg------------------------------dINSLITEISSKFG--LEIKIDKIY 596 Sulfolobus tokodaii
NP_614322 587 RIAEEKyGLKVVYGDTDSLFVKLPdadle----------------------etierVKEFLKEVNGRLP--VELELEDAY 642 Methanopyrus kandl...
YP_254794 551 KIVKES-GFQVIYADTDLMFFKGEn------------------------------dPKKLEEDIANRLS--LNLKFNKFY 597 Sulfolobus acidoca...
YP_919805 562 KKAQSL-GLSIIYGDTDSIFVQFDee-----------------------------kIGRLVEYVEKELG--FEIKLDKVY 609 Thermofilum penden...
YP_687422 550 DIAIEM-GLQVLYGDTDSLFVEMEdnkr------------------------lmdvVRQYIQRVKAELP--LDMDIDNVY 602 uncultured methano...
Feature 1                                                                                     
1D5A_A    584 RRGFFV-TKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEeAVRIVKEVTEKLSRHEVPPEKLVI 662 Desulfurococcus sp...
AAA72443  644 KRGLFV-TKKKYALIEDDGHIVVKGLEVVRRDWSNIAKDTQQAVIRALLEDGDVNlAKKIIKNTIDNLKKGNIDKNDLLI 722 Methanococcus voltae
BAA07580  615 KKVFFTeAKKRYVGLLEDGRIDIVGFEAVRGDWCELAKEVQEKAAEIVLNTGNVDkAISYIREVIKQLREGKVPITKLII 694 Pyrodictium occultum
3122019   583 SAIFFV-EKKRYAGLTEDGRLVVKGLEVRRGDWCELAKKVQREVIEVILKEKNPEkALSLVKDVILRIKEGKVSLEEVVI 661 Archaeoglobus fulg...
BAA75663  584 RRVFFTeAKKRYVGLTVDGKIDVVGFEAVRGDWSELAKETQFKVAEIVLKTGSVDeAVDYVRNIIEKLRRGQVDMRKLVI 663 Aeropyrum pernix
NP_378066 597 KRVFFTeNKKRYAGLTEDGKIDIVGFEAVRGDWCDLAKQVQTNVIELILKSGKVEdAIKYVKTVIFDLRRYNFRIEDLII 676 Sulfolobus tokodaii
NP_614322 643 KRILFV-TKKKYAGYTEDGKIVTKGLEVVRRDWAPIARETQRRVLKRILADNDPEaALKEIHEVLERLKSGDVDIDELAV 721 Methanopyrus kandl...
YP_254794 598 TKLILLeGKKQYAALTKDNKVDMVGIEDYRNNWCDLAKEVLQNVVDQVLRSDKINeAVRYVKSVIYSLRRGEFKIEDLVT 677 Sulfolobus acidoca...
YP_919805 610 EKVFFTeSKKKYCGLLADGRVDLVGFEAVRGDWAEISKEIQERVVEIVLKEEDPWkAVDFVRKTITELSEGRIPLEKLVI 689 Thermofilum penden...
YP_687422 603 RIIFFTeSKKRYAGLTDRGEIVVRGLEVRRGDWCEIAKELQSEVIRIILEEENPDkAAKFVKDTVQKVKSGKVPLDALVI 682 uncultured methano...
Feature 1                                                                                     
1D5A_A    663 Ye-----------aGPHVAAA-------------ATVISYIVLKGPGRVGDRAIPFDEfd--------------paKHRY 704 Desulfurococcus sp...
AAA72443  723 HtqltknieeykstAPHIEVAkkikqr-gdsvrvGDVISYIIVKGSRSISERAELLEY------------------AGDY 783 Methanococcus voltae
BAA07580  695 WktlskrieeyehdAPHVMAArrmkea-gyevspGDKVGYVIVKGSGSVSSRAYPYFMv----------------dPSTI 757 Pyrodictium occultum
3122019   662 YkgltkkpskyesmQAHVKAAlkarem-giiypvSSKIGYVIVKGSGNIGDRAYPIDLiedfdgenlriktksgieIKKL 740 Archaeoglobus fulg...
BAA75663  664 WktltrppsmyearQPHVTAAllmera-gikvepGAKIGYVVTKGSGPLYTRAKPYFMa----------------sKEEV 726 Aeropyrum pernix
NP_378066 677 WktidknldeydvtAPHVVAAkkaaka-gylvskGVKIGYVIVKGSGKISDKAEPYFLik---------------eKNKI 740 Sulfolobus tokodaii
NP_614322 722 TsqltkkpseyvqkGPHVRAAlrlarhlgvepepGTIVRYVIVRGPGSVSDKAYPVELvr--------------eeGKEP 787 Methanopyrus kandl...
YP_254794 678 WniidkdieeykfdLPHIVAArkamks-ghlvtrGSKIGYVIVKGSGKLSNRAEPYFMvk---------------eKSKV 741 Sulfolobus acidoca...
YP_919805 690 WktlskdldeyevdAPHVVVArelkrl-gyrvgkGAKIGYIVVKGAGKVSEKAKPLISvk---------------sPDEV 753 Thermofilum penden...
YP_687422 683 HktltksvtryesaQAHVKAAeramer-dmaaeiGNKISYVIVKGTGTLSDRAYPVDMfhkfkds----klyakdkTYEI 757 uncultured methano...
Feature 1                                   
1D5A_A    705 DAEYYIEnQVLPAVERILR-AFGYRKEDLR 733 Desulfurococcus sp. Tok
AAA72443  784 DINYYIDnQVLPPVIRIME-SLGISEDELK 812 Methanococcus voltae
BAA07580  758 DVNYYIDhQIVPAALRILS-YFGVTEKQLK 786 Pyrodictium occultum
3122019   741 DKDYYIDnQIIPSVLRILE-RFGYTEASLK 769 Archaeoglobus fulgidus
BAA75663  727 DVEYYVDkQVVPAASAHTSsNFGVIEKRLK 756 Aeropyrum pernix
NP_378066 741 DVEYYIDkQIIPVAMRILE-GFGVKESSLK 769 Sulfolobus tokodaii
NP_614322 788 DVDYYIEhQILPAVERIMR-AIGYSRGQIV 816 Methanopyrus kandleri AV19
YP_254794 742 DIEYYIDkQIIPSALKVLG-LFGVKENTFK 770 Sulfolobus acidocaldarius DSM 639
YP_919805 754 DTDYYVKrQIVPAALRILE-YFGVKEEHFS 782 Thermofilum pendens Hrk 5
YP_687422 758 DADYYVDkQLIPTALRILG-YFGYTEDALK 786 uncultured methanogenic archaeon RC-I

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