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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  ####                                                                  
1S5J_A       186 EIPKIKRVAIDIEVYTPvkgRIPDSQKAefPIISIALAGsDGLKKVLVLnrndvne-----gsvkldGISVERFNTEYEL 260
gi 156937483 259 PPPTVKAIAIDIEVFTPaigRIPDPETAqyPVISVALSSnDGLKKVLVLirenlkltedqlkelaeeDYEVEFYDSEKSM 338
gi 807828    257 PPPKPRRLAVDIEVFTPfkgRIPDPSTAsyPVISVAMSSdEGWRAVYVLarpgvpmn--pprgplpeNLHVEIFDDERAL 334
gi 126465771 199 KPPKAKRIAIDIEVYTPfkgRVPNPSLAeyPIISIALVGtDNYRRVLVLaretmwge---lseeyphNAEIEIFDSEEAL 275
gi 14600448  306 PPPKLPLIAFDIEVYSPiatRLPDPSTApyPVISAATADsSGRSRVVLLyrdgvef----tegalpeGTEVEIYDSERAM 381
gi 74501830  192 PIPRIRRLSFDIEVDSEe-gRIPDPKISdrRVTAVGFAAtDGLKQVFVLrsgaeeg-----engvtpGVEVVFYDKEADM 265
gi 18313158  212 PIPHLKRVAIDLEVYTPqenKIPDPKNAefEIISVALVGsDGLRRVLLLkrpglei-----dlryrpDYEVLFFDSEYDL 286
gi 119719216 179 PIPRLRRVAIDIEVDSPp-gIVPNPEKAdrAVIAVSYYS-DDRKGVLLLkrsndi------pkleqnDAEITVFENEKEL 250
gi 159040732 215 PVPPLKRIAIDIEVYTPqenKIPNPKEAlyEIIAIGLAGsDGLKRVLVLrrpeilmnaddqgmllsdDVEVMFFDNERDL 294
gi 161528456 197 PIPKIKRLSVDIEVEAEi-gRIPDPKIAekKVTAIGLKGsDGFDQIFVLktegteqg--tneldqniKVTFYDLDKEKEM 273
gi 170290793 178 PSPSMPNAALDIEVLSPl-dKIPDPREPdkPVAAAAIVDsSGRKEVHVLhrggsl------pgelsnGAKLISYESEGRL 250
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        ##  ###                                                         
1S5J_A       261 LGRFFDILLEYPIVLTFNGDDFDLPYIYFRALKLGYfpeEIPIDVAGk-DEAKYLAGLHIDLYKFFFNKAVRNYAFEGKY 339
gi 156937483 339 LIEVMRIIRDYPVLLTYNGDNFDLAYLYNRALKLGIp--KEMIIFKKgsDKFEIKHGIHIDLYRFYDIAAIKTYAFGNKY 416
gi 807828    335 ILEAFRLISNYPVLLTFNGDNFDLPYLYNRAVKLGIpreYIPFRARS--DYVTLEYGFHIDLYKFFSTKAVQAYAFGNAY 412
gi 126465771 276 ILEAIRVMTKYPIVVTFNGDNFDLPYIFHRALRIGIpkeYLPIHFGE--DIVRLETSIHIDLYKFFKNRAIKSYAFGGKY 353
gi 14600448  382 LLDLVRILQRYPLVVSFNGDNFDLPYIARRLEVLGVpreFAPIELKQ--DYATFRRSLHIDLHKLFGIRALQVYAFGNKY 459
gi 74501830  266 IRDALSVIGSYPFVLTYNGDDFDMPYMLNRARRLGVsdsDIPLYMMR--DSATLRHGVHLDLYRTFSNRSFQLYAFAAKY 343
gi 18313158  287 IREVFKIIVQYPIVITFNGDNFDLPYLYNRALALGMskeELPIAAKR--DYVSVSPGVHIDTFKFFAIKAIEAYAFGGVY 364
gi 119719216 251 LQAAFKIMTSYPVVLTFNGDNFDLPYLLNRALKLGLreeEIPIEWSPrsDYAEIKGSIHIDLYKFFTNKSMRVYAFGNKY 330
gi 159040732 295 LREFFKTIMAYPILITFNGDSFDLTYIYNRALKLGFrkeELPIILTRd-GEARYVLGVHIDLYKFFNIRAVEVYAFGGKY 373
gi 161528456 274 IYDAFKIIKEFPFVVTYNGDEFDLPYLYNRAERLGIkssENPFYMMR--DSATLKHGVHLDLYRTFSNRSFQIYAFSQKY 351
gi 170290793 251 IRSVLDRISEYPLLFTYNGDNFDLPYLARRAKELGVs--DRPVRLEK--DRAILDTGIHIDLYKLFSNRSIQVYVFDNKY 326
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
Feature 1             ##                              #   #           
1S5J_A       340 n--EYNLDAVAKALLGTSKVKVDTLISFL-DVEKLIEYNFRDAEITLQLTTFN 389
gi 156937483 417 k--EVNLDAVAGALLGEHKVQLTKSISEL-NYYELAHYNFRDANLTLKLFTFN 466
gi 807828    413 q--EFTLDAIASALLGEHKVEVESTVSDL-PFFELVRYNVRDADLTLRLTTFN 462
gi 126465771 354 q--EENLDAIATALLGISKIGVEGNIGEL-SLANLVAYNYRDAEITLMLTLFN 403
gi 14600448  460 r--ELSLESISRALLGKGKVELKAPVSEL-NLNKLIEYNLQDARLTLELLTFS 509
gi 74501830  344 t--DYSLNSVTKAMLGEGKVDYGVKLGDL-TLYQTANYCYHDARLTLELSTFG 393
gi 18313158  365 r-gERGLDGIAYAILGIGKVERQKNISRM-NYWELAEYNYRDALITLYFTMYN 415
gi 119719216 331 r-eGRTLDEVSMALLGIGKVKHEEAISEM-TPERLVEYSLRDAELTYKLTSFN 381
gi 159040732 374 sggEKTLDAIASALLGISKVEREKPISEM-NYIELVNYNFRDALLTLYLTTFN 425
gi 161528456 352 t--NFSLNEVSKALLGKEKIDYGLEFDQL-TLYQTANYCYNDALLTYELTSFN 401
gi 170290793 327 a--GYTLDEVADAILGEKKMELESRDFYSvETRTLAEYCLKDAELTFRLGNIG 377

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