Conserved Protein Domain Family
DNA_polB_like1_exo

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cd05782: DNA_polB_like1_exo 
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases
A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. 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 exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Statistics
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PSSM-Id: 99825
View PSSM: cd05782
Aligned: 32 rows
Threshold Bit Score: 173.58
Threshold Setting Gi: 163782354
Created: 15-Nov-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
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            ####                                                                        
gi 114320509   3 VLVFDIETVPDvvggrrllg---ldpslsdqEVAEAMMALrr-----------qsAGTDFQRLHL-----HRIVAISIAa 63
gi 91214924   10 ILFLDIETVPEhsdfedlsp---tkqklftdKTEYQRKEDysp---------keyYERAGIWAEF-----GKIVCISVGy 72
gi 171326852  10 ILFIDIETVPCvadye----------nltapQKLLWGKKAtllgatdtqeignlfSERAGVYAEF-----GKVIVIGLGh 74
gi 124003002  16 ILFVDIKTVSQsdsyht--------lpqnlqKFWDKRFAYrrdedl---nieehyFQQASLQAEF-----GKIVTIGVGy 79
gi 86159259   25 FVTLDLETVPDealvsavdgepsrpyseqlrRVLAERRARt-------------gGRSDFLPLPY-----HRPVAACLLe 86
gi 163782354   4 AIIFDIETVPTkeenlkeed---weyifkyaDTEEDREKQ---------------KERLSLWALT-----AHLVSVALLn 60
gi 21674510    9 VVVFDVEWVPDpasgrriyk---ipdtasddEVLDVMWRKg-------------gATPDDPRPYLkt-vmCRVISIAALv 71
gi 117926920   9 VWAFDAEWTPDplagrmlyn---ldedltdaQVLAEMWKQg--------------GATEENPTPYlktalCRFISIAAVv 71
gi 126646882  11 ILFLDIETASLsdkfen--------lpprlqDEWIKKEKLiqtengk-iepgalyFDRAGIHAEF-----GQVICVGVGy 76
gi 149924378 129 TLVFDIETVPAvdleta--------pesvtkAVHRAADRYdg-----------dtSKVMGLSPFY-----GKVVSIAVGd 184
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 114320509  64 d----ldRHGFRVws-------------lGDPEDDE--------------------AELIRRFFDGVERy----APRLVS 102
gi 91214924   73 fn---fkGNERKFr---------------TTSFYGEe-------------------TDLLKRFKLLVENyfslpHHLMCG 115
gi 171326852  75 itfdicgDPSLQVq---------------ALSSHNE--------------------KELLGQLRNILEEkyqqeNIRLCA 119
gi 124003002  80 fyldehkETALRVk---------------AFAGADE--------------------KGLLEDFKALIDTkf-tdNLVMCA 123
gi 86159259   87 ae---edGGIVRV----------------TDAVAWTd------------------rRGPEAAFLETMWQrl--eGASLVT 127
gi 163782354  61 ------vSEGLALvmylsdrdskeelelrEEFEGGElelrvhmvgfsmeegieeaeRRILTKFWKKAKEk---eGYRFVS 131
gi 21674510   72 rkr-vkdGVTLKLi---------------SLPGLNVseq---------------aeGEIIRQFLEAVGKq----KAQIVG 116
gi 117926920  72 rr--qhqDGTITV----------------TLMSLPEevadtq--------apyakeDAVLSRFLQGVGEk----KPQLVG 121
gi 126646882  77 fqw-kkkDKKLIFr---------------SKVFSNEd------------------eRELLLDFNTLLEKk----KWILCA 118
gi 149924378 185 ge---dpDGPVTAlvva--------ppgrEDDAYPEwirp-------------mteAQLLRSFWHLADS-----AEVVVS 235
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        ##  ###                                                           ##            
gi 114320509 103 WNGGGFDLPVLHYRALLHGitaRRYWDSGqedrdfrfnnylNRFHDR-HTDLMDVLAGYqa-raNAPLDEIATLLGy-PG 179
gi 91214924  116 HNAKEFDFPYIARRMLIRGialPSQLQFFg----------kKPWEIP-HLDTLELWKFGdy-khYTSLKLLTELFNipSP 183
gi 171326852 120 HNGKEFDFPYLCRRMLVNGislPTVLDCAg----------kKPWEVT-HLDTMEMWRFGdr-ksFTSLDLLANLFGvnSS 187
gi 124003002 124 HNGKEFDYPYLCRRMVIHGvelPLTLNLLh----------kKPWEIP-HLDTLEMWKFGdr-khKTSLSLLATLMDipEV 191
gi 86159259  128 FHGKGFDLPVLELRSLKHAiptPAWFGAA------------RRTGGTeHLDVKELLAGQa---tAAPLDLYAKLVGl-PG 191
gi 163782354 132 FNGRGFDSVFLMLRSFVLGv-kVSRQFIG------------NRYEYRnHLDLLDLLSFHgq-grKYSLEFVCRRLGipSP 197
gi 21674510  117 FNSSNADLPILYQRALANRvsaPTFCHRPdkpwe--gvdyfNRYSDF-SIDLKDLVGGYgk--aMPSLHELASSLGi-PG 190
gi 117926920 122 YNSISADIKAMLQRGIIRGmhqPKFAHRPnkpwe--gvdyfARGGDW-HVDLKEVVSGWgq--fTPSLHEMATLSGi-PG 195
gi 126646882 119 HNGKEFDFPYLCRRMLVQGvtlPEPLQIAg----------kKPWEVR-HLDTLELWKFGdy-khYTRLELLAAVFGipTS 186
gi 149924378 236 FNGRGFDVPFVQTRSLIHGv--PARVDLMs-----------SPFALRpHLDLYRLLAPNrgnpaSASLDVICWSLGieSP 302
                        250       260       270
                 ....*....|....*....|....*....|....*....
Feature 1                                #   #          
gi 114320509 180 KMGMSGgKVWEAVQAGe-LGAVRDYCETDVLNTYLVWLR 217
gi 91214924  184 KDDIDGsQVRDVFYKEkdLDRIVTYCEKDVIAVAQLILK 222
gi 171326852 188 KTLMDGsEVSYFYYVEndLTRIAKYCMQDVIVTSQIFLK 226
gi 124003002 192 ENRLEGqDINKVYHETqdMKQITQGCMRDIEILAKLFLK 230
gi 86159259  192 KEDVAGaDVQALYAEGa-LDRIAGYCMTDVVQTFLLFLR 229
gi 163782354 198 KEDMDGhDVKEYFAKGr-YRDIALYNLKDTIATARIYER 235
gi 21674510  191 KMGIDGaDVIDLWRSGd-IRKIVEYNQFDALSTYLVWLR 228
gi 117926920 196 KMDVAGdQVPQMWLDGr-LADIVAYNEFDALTTYLLWLR 233
gi 126646882 187 KDDLDGsQVNTTFHLEknINRIKKYCRKDVEVTARVYLA 225
gi 149924378 303 KGEMDGsLVAPTYARGd-IEMIATYNVGDVRATRSVYRH 340

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