Conserved Protein Domain Family
DNA_polB_like2_exo

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cd05785: DNA_polB_like2_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: 99828
View PSSM: cd05785
Aligned: 7 rows
Threshold Bit Score: 281.222
Threshold Setting Gi: 116626444
Created: 1-Oct-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:
Feature 1                       ####                                                              
ZP_00592424   169 FKGMVFEDLYRMQLDIETYfkpesgksskveigKDQVIIVSLSDNRGWEKVIHAh---GRTEKELLIELIAIIREKDPDV 245  Prosthecochlo...
NP_954286     131 FKGFEFGHLRRLALDIETScgegfef-snpdreDDRILSIALMEEGGYEAFLSAt---EMDEREMLERLGGIIRERDPDV 206  Geobacter sul...
NP_663155     156 FKGMLFDDLHRLQLDIETYyqpdkkr-kgkgigEDPIIIVSLSDNRSWEHVIHSk---GRSEKDLLEELVHIIRQKDPDV 231  Chlorobium te...
YP_446104     154 LLGMTLDDLHRLQLDIEVYsegsfp---nadrpDDKVIIVALSDNRGWDEVLHLr--dGIGEEQLLQELVYVLQERDPDV 228  Salinibacter ...
YP_828600     145 FRDLTFDHLRRLQFDLETTgld---------agRDRIFMVAVRDPSGAAETLEVegegDAAEADLIRRLVARIQAADPDV 215  Solibacter us...
ZP_01924722    19 FSGMEFSELRRLSFDLETLttpgydf-pnsdreGDEIVIISMRDSTGFELVLSQe---DMSEKELIQAFVKTLAERDPDV 94   Victivallis v...
YP_001819680  113 YRDLMFHDLRRCQLDIETRssddgf--cdparpDDRVLAIGLRCGGHNRLLILEem-tDAAEKKLMEQLNHALAHLDPDV 189  Opitutus terr...
Feature 1            ##  ###                                                                      
ZP_00592424   246 IEGHNIFRFDLPYLHRRCEINGIEFRIGRDQS-IPRNYPASIRFAERSIDY--TFYDIAGRHVIDTWFLVQSFDVSKRAM 322  Prosthecochlo...
NP_954286     207 IEGHNIFRFDLEYIRARAARHGVKLAWGRDGS-IPRVHPSRFSVAERLIDY--PRWDVYGRTVIDTYFLVQIHDVSSRDL 283  Geobacter sul...
NP_663155     232 IEGHNIFGFDLPYLQRRCELNGVRFAIGRNGL-VPRSYPATIRFAERSADF--QFCDIPGRHVIDTYFLVQNYDISKHTL 308  Chlorobium te...
YP_446104     229 IEGHNIFEFDLAYLLDRCALHGVDFAIGRDGS-VPRTYDSSMRFAERTVDY--PAVDIVGRHVIDTYFQVMSFDVFSRDL 305  Salinibacter ...
YP_828600     216 IENHNLHGFDLPFLDRRARRLGVPLSLGRIGPaGLRQRTARRGAAAGLDDRrkVRYVAPGRELIDTLDAVLRHDFSERDL 295  Solibacter us...
ZP_01924722    95 IEGHNLCRFDLPYLEARARRHKVKLALGRDGS-TFSKRSSRFNIADRIINY--SRYDVWGRHVVDTLHLAMLYDGANRNL 171  Victivallis v...
YP_001819680  190 IEGHNIFKFDLDYLRQRCRRFKVPCAWGRYGQ-KATFRNSRLKVAERWIDF--LRCDLPGRAVVDTYLLVQLFDITTREL 266  Opitutus terr...
Feature 1            ##                                      #   #         
ZP_00592424   323 PGYGLKAAAKFFGVAREN---RVYVDYADMADLWENNPEKLLEYALDDVRETREIAS 376  Prosthecochloris aestuarii DSM 271
NP_954286     284 ESYGLKQAAIHFGLAAPD---RVYLDRQAMDEVFRSDPERMKRYNLDDTRETLALSR 337  Geobacter sulfurreducens PCA
NP_663155     309 PSYGLKAVAKFFGFASPN---RTYVDYKNIASTWDDNPETLLAYALDDVRETRELAA 362  Chlorobium tepidum TLS
YP_446104     306 PDYSLKTAARYFDLAPEE---RTYIEGTEIAKAWRTDRATLLEYALDDVIETKRLAG 359  Salinibacter ruber DSM 13855
YP_828600     296 PGHGLKAVARHLGLAGPD---REQIPGRQIYEVYRRDPARVRRYATADVEEVAGLAR 349  Solibacter usitatus Ellin6076
ZP_01924722   172 ESYNLKYLAKHFRIASDE---RTYVDGSKITELWNSDHATLLAYALDDVRETEALSA 225  Victivallis vadensis ATCC BAA-548
YP_001819680  267 TSYGLKEVAVYFGITEEDsltRTYIEGHRIKDVFASDRARFRAYLEDDLRETEGLAA 323  Opitutus terrae PB90-1

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