Conserved Protein Domain Family
DNA_pol_A_plastid_like

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cd08640: DNA_pol_A_plastid_like 
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). The three-dimensional structure of plastid DNA polymerase has substantial similarity to Pol I. The structure of Pol I resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Statistics
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PSSM-Id: 176477
View PSSM: cd08640
Aligned: 11 rows
Threshold Bit Score: 501.541
Threshold Setting Gi: 30020006
Created: 23-Feb-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:The Pol A domain has a shape of a right hand in which the palm, fingers and thumb form the DNA-binding crevice; the active site, composed of three acidic residues, is located at the palm which forms the base of the crevice.
  • Citation:PMID 9857206

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
AAL58915      638 GWPSVGGDVLKELAGKVSAEYDFMDdvsdisleevvedddvetsetqksktddetdtsaygtayvafgggergkeaCHAI 717  thale cress
EER03934      560 GWPKVESAILRAFAGEPHEGNYGVAyqqlepvr-----------------------------------ghehaasvCRLL 604  Perkinsus mar...
XP_647557     987 GWPSVDSSSLRELAGKNPIDGKYGSaydffvksknecyk-----------------------dlpieereqmgreaSIAI 1043 Dictyostelium...
XP_002294547  369 GAPSATADVLRKLAGDPFADPPKYGaayeffgg------------------------------------geagheaCVAF 412  Thalassiosira...
XP_001785330  382 GWPAVGGAAIKALAGKVAIDYAALEedsevedmddieeseslltsagvet-eheedlsvygkayqafggglegkeaCMAL 460  Physcomitrell...
CAL55440      568 GLPAVSSVVLRSLAGKPGAARAIMDawdtlsdeekseealkka----------------cggafdafgggqegvqaCAAI 631  Ostreococcus ...
EEY65558      677 GLPAASAEVLKDLAGHPEANPPQYGrayghfed------------------------------------keegaaaCVAL 720  Phytophthora ...
XP_001431083  485 GMPQADYNALKQLAGDVEKQQYGLIyhhfagkg-----------------------------------epqkgidaCVAI 529  Paramecium te...
NP_831637     399 TGASLDQEALIDMAFMLENKLNDIDeekylgvslpenwenidpekdpt-----ldklergairiakrephpykeqaLEVI 473  Bacillus cere...
YP_001681418  282 KLPVFKTTAKYQEAMDDEAMILLSEwcren------------------------------------------rpelAELF 319  Heliobacteriu...
ZP_02865851   288 RLPVLKICEKGEPSLDDESLILLDEwclrn------------------------------------------fkkgTYLI 325  Clostridium p...
Feature 1               #   #  ##                           ### # ####                            
AAL58915      718 ASLCEVCSIDSLISNFILPLQGsnv--sgKDGRVHCSLNIN-TETGRLSARRPNLQNQPALEKDRYKIRKAFVASPGNTL 794  thale cress
EER03934      605 WHLQRSIRISAAITSVLSPLIErikydedGFGRIHPSLALD-TTTGRLCCRKPNLQNPPSAHNDLYSIRKAFSARPGNTL 683  Perkinsus mar...
XP_647557    1044 NALLELGSIGTLLNTFIIPLQKla----dSNSRLHTSINVN-TETGRLSSKKPNLQNQPALEKDRYKIRKAFTCEPGNTL 1118 Dictyostelium...
XP_002294547  413 FSLTAIGSIDTMIANFLTSLQTla----dDQNRVHCSLNIN-TETGRLSSRKPNMQNQPALEKDKYKIRQAFMASPGNNL 487  Thalassiosira...
XP_001785330  461 AALCEVASINTLLSNFIEPLQGndi-ksaSDGRVHCSLNIN-TETGRLSARRPSLQNQPALEKDRYKIRQAFVAAPGKSL 538  Physcomitrell...
CAL55440      632 DALNDVAAIDTLLSNFIIPLQGddi--rgPEGRVHGALNIN-TETGRLSARRPSLQNQPALEKDRYGIRKAFTAGPGNVL 708  Ostreococcus ...
EEY65558      721 KALFDISSINTMLNNFILPLQEla----dSNSRVHCSLNLN-TDTGRLSSRKPNLQNQPAMGKDRYKIRDAFTAPPGKKL 795  Phytophthora ...
XP_001431083  530 NDLLELKSIEVLLHTFIIPLIElt----dPSGRIHTSININ-TETGRLSSRNPNLLNQPALEKDRYKIRKSFIAKKGNKL 604  Paramecium te...
NP_831637     474 DQLKKIQKYTTLLSSHIIGREKyl---nfMSGRIHAGYSPF-TETGRLNSFNPNGQNVPRPDNDEFKIRNFFVPKPGKIL 549  Bacillus cere...
YP_001681418  320 ELVQEYRRWGKIKSTYIDGYLEyi---nsVTGRIHPDMFPLgTETGRFAARNPNLQNCPRKDNDPVGVRNFFIAPKGKAL 396  Heliobacteriu...
ZP_02865851   326 ECIKRHKRVSKLKSTYIEALGKll---ncETGKIHTDFFSMgTETGRFSSRNPNLQNLPRKDNDHLGIRKLFIPSPNHVF 402  Clostridium p...
Feature 1            ##                           #                                               
AAL58915      795 VVADYGQLELRILAHLTGCKSMMEAFKAGGDFHSRTAMNMyphvreavengqvilewhp--epgedkppvpllkdafgsE 872  thale cress
EER03934      684 IVGDYSQLELRILAHMSRCESMIRQLNQGGDIHSQCAVDLfpevaeavangsvvidd------aeahpgipsvktkfstQ 757  Perkinsus mar...
XP_647557    1119 IVADYGQLELRLLAHITNCKSMITAFQVGGDFHSRTAMGMyphvkeaidrgevllew-----dgegeppkpllknvyasE 1193 Dictyostelium...
XP_002294547  488 IVADYGQLELRLLASMTDCTSMIDAFEAGGDFHSRTALGMfkyiqdavangdvllewd----yskgeppkpmlkdqyasE 563  Thalassiosira...
XP_001785330  539 VVADYGQLELRLLAHLADCKSMKAAFKAGGDFHSRTAMNMyphvreavekervllew-----eshgkppapllkdifgsE 613  Physcomitrell...
CAL55440      709 VVADYGQLELRLLAHMAGCKSMQEAFEAGGDFHSRTALGMysnikdaiakgevvleygeqeegvdekdrpalvkdvfasE 788  Ostreococcus ...
EEY65558      796 IVADYSQLELRLMAHITQCKAMIEAFKAGGDFHSRTAMGMypyvakavengeallewd---httgkeppapllkdkygdE 872  Phytophthora ...
XP_001431083  605 IVADYGQLELRVLAHMTKCKAMIDAFLKGGDFHSRTVITMfphiqeeidkgelliewd----kskgkapaplvkdkyaaE 680  Paramecium te...
NP_831637     550 FFIDFSGFELRLMAWKSGDEVMTELFNTGGDMHRRTASVMtgksea----------------------------eivkkE 601  Bacillus cere...
YP_001681418  397 LSLDFSQIELRVGAFYCRDERMLETYRTGGDIHAQTTSVIyripfeeaa---------------------dksaqhykeR 455  Heliobacteriu...
ZP_02865851   403 LDFDFSQIELRVGAYYCRDRKMINAFMKDFDIHGITTSIIynipleeat---------------------drnhedfkkR 461  Clostridium p...
Feature 1         #   #                                                                           
AAL58915      873 RRKAKMLNFSIAYGKTAVGLSRDWKvs------tkEAQETVDLWYNDRQEVRKWQEMRKKEAIEDGYVLTLLGRSRRFPA 946  thale cress
EER03934      758 RQQAKVMNFSIAYGKTERTLAEEMDlp------vtDIRDMFTRWNNSKKGVERWKAEIIQQARDTQHATSVLGRHRRFPH 831  Perkinsus mar...
XP_647557    1194 RRKAKTLNFSIAYGKTAHGLSQDWGvt------lnEAKETLNRWYEDRPEVLVWQRKTIETAHKYGWTRTLMGRYRQLPD 1267 Dictyostelium...
XP_002294547  564 RRKAKTLNFSIAYGKTAHGLSQDWGvs------lkEAEEMLRAWYDSRPEVEKWQQNTKKAARNYGITRTLMGRYRHLPH 637  Thalassiosira...
XP_001785330  614 RRKAKMLNFSIAYGKTAMGLAKDWKvk------vdEAKATVDLWYSDRPEVLAWQKERKQEAHTSLRVHTLLGRARHLPD 687  Physcomitrell...
CAL55440      789 RRKAKVLNFSIAYGKTAHGLSKDWGts------leEAANTVELWYSDRPEVRDWQEVQKKMAVEKNLVRTLLGRVRNLPD 862  Ostreococcus ...
EEY65558      873 RKNAKVLNFSIAYGKTAFGLAKDFNvs------rkEAADTLEKWYSDRGEVRDWQKKAIETARTFGYTRTLLGRYRRLPD 946  Phytophthora ...
XP_001431083  681 RRKAKVLNFSIAYGKTATGFAKDWQce------vkEAQKTIDAWFAQRKEVEQWQYNVRMIAKNQFFTQTLLGRYRYLEK 754  Paramecium te...
NP_831637     602 RTDAKAGNFGISYGGTEHALQFTFKtkymirktldECAQIVNAVKTAYKRIPEYQRKIVLEAREQGYVQTIYGYMRLLPG 681  Bacillus cere...
YP_001681418  456 RAIAKNCNFGVFYGLFPKGLHRNLKfkagldtplsECERIIANLKAGYPRLVQWQEKTKKRAASRRYTETWLGRRRYLPD 535  Heliobacteriu...
ZP_02865851   462 RTIAKNCNFGVFFGLFPKGLQKTLMykgginisekDCERIIRNIKDGYPRLSTWQKDTVKVAAYRGYTRSRTGRRRYLKD 541  Clostridium p...
Feature 1                            #      #                                   ###               
AAL58915      947 sksr-------aqrnHIQRAAINTPVQGSAADVAMCAMLEISINqq-----lKKLGWRLLLQIHDEVILEGPIe--sAEI 1012 thale cress
EER03934      832 ikhrl-----rkysgRSERAAVNFVIQGSAADIAMMAMLRVDRDer-----lRRMGFKIVMQVHDEVILEGPAe--nATD 899  Perkinsus mar...
XP_647557    1268 ikgnk------gmkgHAERASINTPLQGGAADIVMKAMLIIEDNkr-----lKELGFKLIMQIHDELILEGPEq--hADE 1334 Dictyostelium...
XP_002294547  638 amegnn----rkrlgHAERASINTPIQGGAADVAMMAMIKINDSll-----lKKLGWILLMQVHDEVILEGPEe--tAEE 706  Thalassiosira...
XP_001785330  688 inssn-----allrsHMERAAINTPVQGSAADVAMCAMLEINRNsk-----lRELGWKLLLQVHDEVILEGPSe--sAQE 755  Physcomitrell...
CAL55440      863 asskn-----eafksHALRASINTPIQGGAADIAMLAMLQIQRCpr-----lKELGYKLLMQIHDEVILEGPEe--hKDE 930  Ostreococcus ...
EEY65558      947 amlrddsmtskkargHAERAAINTPIQGAAADVVMQAMLQVHHSpr-----lRELGWGMVSQIHDEIIVEGPEe--sVDE 1019 Phytophthora ...
XP_001431083  755 yfqqqt----rsyinHGLRAAINTPIQGGAADIVIAAMVKIYKNqs-----lKDLGYKLLLQVHDELILEGPEe--nAQE 823  Paramecium te...
NP_831637     682 insan-----rrdrgSAERQAANTPVQGSAADIMKKVQNEIYESigkqegvlSHGSADMIAQIHDEIIFEIDDdpeiVVA 756  Bacillus cere...
YP_001681418  536 iassd-----wgkksFAERCALNTPIQGTAADILKLALGRIIEGl------pQRMRLRPVLQIHDELVFEVPEd--kVHE 602  Heliobacteriu...
ZP_02865851   542 ikskd-----wnkraVSERCALNTPIQGTAADIIKIAMARILREl------pEREYIKPLLQIHDELLFEVREd--kVNE 608  Clostridium p...
Feature 1                                               
AAL58915     1013 AKDIVVDCMSKPFngr---niLSVDLSVDAKCAQNWYA 1047 thale cress
EER03934      900 AVPIVRDLMEHPFadikpdyrMLINLDVDIATGTNWSD 937  Perkinsus marinus ATCC 50983
XP_647557    1335 ARSIMMNLMSNPLtt-----pLLIDLVVDCRYAKTWYD 1367 Dictyostelium discoideum AX4
XP_002294547  707 AFEEVVKCMQEPWvlg--ldkTKVPLLVDGSFKHNNWY 742  Thalassiosira pseudonana CCMP1335
XP_001785330  756 AKELVIKSMMYPFnge---nfLDVELVVDGDYAESWYA 790  Physcomitrella patens subsp. patens
CAL55440      931 ALALTKYHMENPFpgh--vnlLDVALAVDGDYAKTWYD 966  Ostreococcus tauri
EEY65558     1020 AMKLVVHLMENPFqk-----pLSVALEVDANVDDSWFK 1052 Phytophthora infestans T30-4
XP_001431083  824 ALKIVKELMENPFei-----qLELPLEVDAKIGNNWYE 856  Paramecium tetraurelia strain d4-2
NP_831637     757 VEKQIKQVMEQPPvp-----gFPVPIEAEGSVGYRWGE 789  Bacillus cereus ATCC 14579
YP_001681418  603 AAVFIKSCMEERPfe-----eFDVPIVAEAAFGVRFGE 635  Heliobacterium modesticaldum Ice1
ZP_02865851   609 AIAFIKDCMERTPfk-----dFNIPLKVEYSVGYNFDE 641  Clostridium perfringens C str. JGS1495

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