1S5J,1Q8I,1QHT,1CLQ


Conserved Protein Domain Family
DEDDy_DNA_polB_exo

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cd05160: DEDDy_DNA_polB_exo 
Click on image for an interactive view with Cn3D
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases
The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. 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. This 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 contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia 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. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Statistics
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PSSM-Id: 176646
View PSSM: cd05160
Aligned: 20 rows
Threshold Bit Score: 161.754
Threshold Setting Gi: 68553042
Created: 26-Apr-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.
  • Structure:1CLQ_A; Enterobacteria phage RB69 family-B DNA polymerase exonuclease domain binds two calcium ions and the 3 'end of primer DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9888810

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                 ####                                                                        
1S5J_A            192 RVAIDIEVYtpvkgrip----dsqkaefPIISIALAGs-------------DGLKKVLVLnrndvnegsv---------- 244  Sulfolobu...
1QHT_A            137 MLAFAIATLyhege---------efgtgPILMISYAD--------------GSEARVITWkkidlp-------------- 179  Thermococ...
1CLQ_A            110 VANFDIEVTspdgfpe------psqakhPIDAITHYDs------------iDDRFYVFDLlnspygnveewsieiaaklq 171  Enterobac...
REF_jgi:Mlg_1353    3 VLVFDIETVpdvvggrrllgldpslsdqEVAEAMMALrr----------qsAGTDFQRLHlhrivaisiaadld------ 66   Alkalilim...
P33609            543 VMSFSMKTMqnvq-----------nhqhEIIAMAALVhh----------sfALDKAPPEPpfqthfcvvskpkdcifp-- 599  house mouse
NP_001087694      317 VLSFDIECAgrkgvf-------pepdkdPVIQIANMVl------------rQGEKDPFIRnvftlgtcas---------- 367  African c...
ZP_00592424       179 RMQLDIETYfkpesgks---skveigkdQVIIVSLSDn-------------RGWEKVIHAh------------------- 223  Prostheco...
Q07864            271 VLAFDIETTklplkf-------pdaetdQIMMISYMId------------gQGYLITNREivsediedfeftp------- 324  human
O60673           2307 RTRRDLEPDpe---------------fdPICALFYCIssdtplpdtektelTGVIVIDKDktvfsqdiryqtpl------ 2365 human
NP_615844         194 YLAFDIECLpldggm-------pspdvsPIIMISFSFep----------eyKGHKTLILLakpaagm------------- 243  Methanosa...
Feature 1                                                         ##  ###                             
1S5J_A            245 ----------kldgisverfNTEYELLGRFFDILLE--YPIVLTFNGdDFDLPYIYFRALKLGyfp------------ee 300  Sulfolobu...
1QHT_A            180 ---------------yvdvvSTEKEMIKRFLRVVREkdPDVLITYNGdNFDFAYLKKRCEELGikftl--------grdg 236  Thermococ...
1CLQ_A            172 eqggdevpseiidkiiympfDNEKELLMEYLNFWQQktPVILTGWNVeSFDIPYVYNRIKNIFgestak------rlsph 245  Enterobac...
REF_jgi:Mlg_1353   67 -------rhgfrvwslgdpeDDEAELIRRFFDGVERy-APRLVSWNGgGFDLPVLHYRALLHGita-------------r 125  Alkalilim...
P33609            600 ---cdfkeviskknmkveiaATERTLIGFFLAKVHKidPDILVGHNIcSFELEVLLQRINECKvpyws---------kig 667  house mouse
NP_001087694      368 -----------ivgsqvlcfEREDALLKAWAEFVRIidPDIITGYNIqNFDMPYLINRAQTLKvst------------fp 424  African c...
ZP_00592424       224 -------------------gRTEKELLIELIAIIREkdPDVIEGHNIfRFDLPYLHRRCEINGief-------------r 271  Prostheco...
Q07864            325 -------kpeyegpfcvfnePDEAHLIQRWFEHVQEtkPTIMVTYNGdFFDWPFVEARAAVHGls--------------- 382  human
O60673           2366 ------lirsgitglevtyaADEKALFHEIANIIKRydPDILLGYEIqMHSWGYLLQRAAALSidlc-----------rm 2428 human
NP_615844         244 -------------dgdvlscMDETEMLNKFFEIICEydPDIVAGYNHqDFDIPYITERVKALVakgetinsvvgrdgspi 310  Methanosa...
Feature 1                                                                          ##                 
1S5J_A            301 iPIDVAg-------------------kDEAKYLAGLHIDLYKFFfnkavrnyafegkyneyNLDAVAKALLgt--sKVKV 359  Sulfolobu...
1QHT_A            237 sEPKIQrmg----------------drFAVEVKGRIHFDLYPVIrrtin--------lptyTLEAVYEAVFgk--pKEKV 290  Thermococ...
1CLQ_A            246 rKTRVKvienm------------ygsrEIITLFGISVLDYIDLYkkfsft------nqpsySLDYISEFELnv--gKLKY 305  Enterobac...
REF_jgi:Mlg_1353  126 rYWDSGqedrdf---------rfnnylNRFHDRHTDLMDVLAGYqar-----------anaPLDEIATLLGyp--gKMGM 183  Alkalilim...
P33609            668 rLRRSNmpklgs----------rsgfgERNATCGRMICDVEISAkelih--------cksyHLSELVQQILk---tERIV 726  house mouse
NP_001087694      425 fLGRIRslksvirdssfqskqmgrrenKVINTEGRVQFDLLQVLlrdyk--------lrsyTLNAVSFHFLqe--qKEDV 494  African c...
ZP_00592424       272 iGRDQSiprnypasi---rfaersidyTFYDIAGRHVIDTWFLVqsfdvsk----rampgyGLKAAAKFFGvarenRVYV 344  Prostheco...
Q07864            383 mQQEIGfqk---------------dsqGEYKAPQCIHMDCLRWVkrdsyl------pvgshNLKAAAKAKLgy--dPVEL 439  human
O60673           2429 iSRVPDdkienrfaae--rdeygsytmSEINIVGRITLNLWRIMrneva--------ltnyTFENVSFHVLhq--rFPLF 2496 human
NP_615844         311 gYRKFGl-------------------iTRTEMKGRVVVDALPLVrrafs--------lkqyTLRAVSKELLsr--eKLDV 361  Methanosa...
Feature 1                                   #   #         
1S5J_A            360 DTlis--------fldVEKLIEYNFRDAEITLQLTT 387  Sulfolobus solfataricus
1QHT_A            291 YAeeiaqa--wesgegLERVARYSMEDAKVTYELGR 324  Thermococcus sp.
1CLQ_A            306 DGpiskl-----resnHQRYISYNIIDVYRVLQIDA 336  Enterobacteria phage RB69
REF_jgi:Mlg_1353  184 SGgkvwea---vqageLGAVRDYCETDVLNTYLVWL 216  Alkalilimnicola ehrlichei MLHE-1
P33609            727 IPtenirnm-ysessyLLYLLEHIWKDARFILQIMC 761  house mouse
NP_001087694      495 QHsiitdlq-ngneqtRRRLAVYCLKDAYLPLRLLE 529  African clawed frog
ZP_00592424       345 DYadmad----lwennPEKLLEYALDDVRETREIAS 376  Prosthecochloris aestuarii DSM 271
Q07864            440 DPedmcr----mateqPQTLATYSVSDAVATYYLYM 471  human
O60673           2497 TFrvlsdwfdnktdlyRWKMVDHYVSRVRGNLQMLE 2532 human
NP_615844         362 PPlemeehw-ndsgdkFRKFVDYARRDSELALELVL 396  Methanosarcina acetivorans C2A

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