1S5J


Conserved Protein Domain Family
DNA_polB_B1_exo

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cd05783: DNA_polB_B1_exo 
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DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases
The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.
Statistics
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PSSM-Id: 99826
View PSSM: cd05783
Aligned: 11 rows
Threshold Bit Score: 296.538
Threshold Setting Gi: 170290793
Created: 1-Oct-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site includes the catalytic site (characterized by four invariant acidic residues, DEDD) and the substrate (ssDNA) binding site.
  • Citation:PMID 9888810

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                  ####                                                                  
1S5J_A       186 EIPKIKRVAIDIEVYTPvkgRIPDSQKAefPIISIALAGsDGLKKVLVLnrndvne-----gsvkldGISVERFNTEYEL 260  Sulfolobus sol...
YP_001435279 259 PPPTVKAIAIDIEVFTPaigRIPDPETAqyPVISVALSSnDGLKKVLVLirenlkltedqlkelaeeDYEVEFYDSEKSM 338  Ignicoccus hos...
BAA07579     257 PPPKPRRLAVDIEVFTPfkgRIPDPSTAsyPVISVAMSSdEGWRAVYVLarpgvpmn--pprgplpeNLHVEIFDDERAL 334  Pyrodictium oc...
YP_001040880 199 KPPKAKRIAIDIEVYTPfkgRVPNPSLAeyPIISIALVGtDNYRRVLVLaretmwge---lseeyphNAEIEIFDSEEAL 275  Staphylothermu...
NP_146963    306 PPPKLPLIAFDIEVYSPiatRLPDPSTApyPVISAATADsSGRSRVVLLyrdgvef----tegalpeGTEVEIYDSERAM 381  Aeropyrum pern...
O31096       192 PIPRIRRLSFDIEVDSEe-gRIPDPKISdrRVTAVGFAAtDGLKQVFVLrsgaeeg-----engvtpGVEVVFYDKEADM 265  Cenarchaeum sy...
NP_559825    212 PIPHLKRVAIDLEVYTPqenKIPDPKNAefEIISVALVGsDGLRRVLLLkrpglei-----dlryrpDYEVLFFDSEYDL 286  Pyrobaculum ae...
YP_919711    179 PIPRLRRVAIDIEVDSPp-gIVPNPEKAdrAVIAVSYYS-DDRKGVLLLkrsndi------pkleqnDAEITVFENEKEL 250  Thermofilum pe...
YP_001539984 215 PVPPLKRIAIDIEVYTPqenKIPNPKEAlyEIIAIGLAGsDGLKRVLVLrrpeilmnaddqgmllsdDVEVMFFDNERDL 294  Caldivirga maq...
YP_001582282 197 PIPKIKRLSVDIEVEAEi-gRIPDPKIAekKVTAIGLKGsDGFDQIFVLktegteqg--tneldqniKVTFYDLDKEKEM 273  Nitrosopumilus...
YP_001737609 178 PSPSMPNAALDIEVLSPl-dKIPDPREPdkPVAAAAIVDsSGRKEVHVLhrggsl------pgelsnGAKLISYESEGRL 250  Candidatus Kor...
Feature 1                        ##  ###                                                         
1S5J_A       261 LGRFFDILLEYPIVLTFNGDDFDLPYIYFRALKLGYfpeEIPIDVAGk-DEAKYLAGLHIDLYKFFFNKAVRNYAFEGKY 339  Sulfolobus sol...
YP_001435279 339 LIEVMRIIRDYPVLLTYNGDNFDLAYLYNRALKLGIp--KEMIIFKKgsDKFEIKHGIHIDLYRFYDIAAIKTYAFGNKY 416  Ignicoccus hos...
BAA07579     335 ILEAFRLISNYPVLLTFNGDNFDLPYLYNRAVKLGIpreYIPFRARS--DYVTLEYGFHIDLYKFFSTKAVQAYAFGNAY 412  Pyrodictium oc...
YP_001040880 276 ILEAIRVMTKYPIVVTFNGDNFDLPYIFHRALRIGIpkeYLPIHFGE--DIVRLETSIHIDLYKFFKNRAIKSYAFGGKY 353  Staphylothermu...
NP_146963    382 LLDLVRILQRYPLVVSFNGDNFDLPYIARRLEVLGVpreFAPIELKQ--DYATFRRSLHIDLHKLFGIRALQVYAFGNKY 459  Aeropyrum pern...
O31096       266 IRDALSVIGSYPFVLTYNGDDFDMPYMLNRARRLGVsdsDIPLYMMR--DSATLRHGVHLDLYRTFSNRSFQLYAFAAKY 343  Cenarchaeum sy...
NP_559825    287 IREVFKIIVQYPIVITFNGDNFDLPYLYNRALALGMskeELPIAAKR--DYVSVSPGVHIDTFKFFAIKAIEAYAFGGVY 364  Pyrobaculum ae...
YP_919711    251 LQAAFKIMTSYPVVLTFNGDNFDLPYLLNRALKLGLreeEIPIEWSPrsDYAEIKGSIHIDLYKFFTNKSMRVYAFGNKY 330  Thermofilum pe...
YP_001539984 295 LREFFKTIMAYPILITFNGDSFDLTYIYNRALKLGFrkeELPIILTRd-GEARYVLGVHIDLYKFFNIRAVEVYAFGGKY 373  Caldivirga maq...
YP_001582282 274 IYDAFKIIKEFPFVVTYNGDEFDLPYLYNRAERLGIkssENPFYMMR--DSATLKHGVHLDLYRTFSNRSFQIYAFSQKY 351  Nitrosopumilus...
YP_001737609 251 IRSVLDRISEYPLLFTYNGDNFDLPYLARRAKELGVs--DRPVRLEK--DRAILDTGIHIDLYKLFSNRSIQVYVFDNKY 326  Candidatus Kor...
Feature 1             ##                              #   #           
1S5J_A       340 n--EYNLDAVAKALLGTSKVKVDTLISFL-DVEKLIEYNFRDAEITLQLTTFN 389  Sulfolobus solfataricus
YP_001435279 417 k--EVNLDAVAGALLGEHKVQLTKSISEL-NYYELAHYNFRDANLTLKLFTFN 466  Ignicoccus hospitalis KIN4/I
BAA07579     413 q--EFTLDAIASALLGEHKVEVESTVSDL-PFFELVRYNVRDADLTLRLTTFN 462  Pyrodictium occultum
YP_001040880 354 q--EENLDAIATALLGISKIGVEGNIGEL-SLANLVAYNYRDAEITLMLTLFN 403  Staphylothermus marinus F1
NP_146963    460 r--ELSLESISRALLGKGKVELKAPVSEL-NLNKLIEYNLQDARLTLELLTFS 509  Aeropyrum pernix K1
O31096       344 t--DYSLNSVTKAMLGEGKVDYGVKLGDL-TLYQTANYCYHDARLTLELSTFG 393  Cenarchaeum symbiosum
NP_559825    365 r-gERGLDGIAYAILGIGKVERQKNISRM-NYWELAEYNYRDALITLYFTMYN 415  Pyrobaculum aerophilum str. IM2
YP_919711    331 r-eGRTLDEVSMALLGIGKVKHEEAISEM-TPERLVEYSLRDAELTYKLTSFN 381  Thermofilum pendens Hrk 5
YP_001539984 374 sggEKTLDAIASALLGISKVEREKPISEM-NYIELVNYNFRDALLTLYLTTFN 425  Caldivirga maquilingensis IC-167
YP_001582282 352 t--NFSLNEVSKALLGKEKIDYGLEFDQL-TLYQTANYCYNDALLTYELTSFN 401  Nitrosopumilus maritimus SCM1
YP_001737609 327 a--GYTLDEVADAILGEKKMELESRDFYSvETRTLAEYCLKDAELTFRLGNIG 377  Candidatus Korarchaeum cryptofilum OPF8

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