3IKM


Conserved Protein Domain Family
DNA_pol_gammaA

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cd08641: DNA_pol_gammaA 
Click on image for an interactive view with Cn3D
Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria
DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into 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), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases 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. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases.
Statistics
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PSSM-Id: 176478
View PSSM: cd08641
Aligned: 17 rows
Threshold Bit Score: 679.041
Threshold Setting Gi: 167521656
Created: 26-Feb-2010
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 22 residues -Click on image for an interactive view with Cn3D
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                                                                                         
3IKM_A        364 GVSYLPVNQN-WERYLAEAQGTYEELQREMKKSLMDLANDACQLlsgerykedpwlwdlewdlqefkqkkakkvkkepat 442  human
Q27607        398 GSAYLPVNSN-WERYIREAQLTYEDLSIEAKYHLGRRAEEACSLllddqyrqnlwlwdedwsvqelklkqppkrkplptv 476  fruit fly
Q12704        387 GSVFLPVNHS-WTRYINGVEEQYQQMIQLVDQKLSQYAEKAKDLintkdtvlkdpwlrqldwtpcnlyrklkkatqevpv 465  fission yeast
XP_001728845  531 GSTFLPLDAT-WTNYQQQAKAKFDEMNANVVTTLKKLTYDLVEAgiqdidrasetpakdrwwetdpwysqldwspkrpkt 609  Malassezia gl...
EDK36807      376 GTLVLPTTKK-WDSYVSTAEDCYLHNRQQVSEILRERANSLVSFveakeplpdvsddpwlrqldwtlkeqrfkkngepva 454  Pichia guilli...
Q9Y767        409 ASVILPVNKT-WDTYIETAEATYLQMLHGVQERLFTLMERTLDYkadpekylsdpwlsqldwsgqeikmakpkkkgdver 487  Neurospora cr...
P15801        379 SKCILPTKLNdWNDYLNSSESLYQQSKVQIESKIVQIIKDIVLLkdkpdfylkdpwlsqldwttkplrltkkgvpakcqk 458  baker's yeast
Q01941        372 SSCILPTTTK-WEDYIETSERLYQESRRMIEKNLHVICEETVKLkddptkpwendpwlsqldwtidpirltkkgeihknq 450  Pichia pastoris
XP_505619     400 SSAILPTDSE-WKDYLNRCENMYQKMKKSIDEGLQSLVTEAVKLkdeadkepwlndpwlsqldwtikpikmvkipakqgg 478  Yarrowia lipo...
XP_001950479  585 GTSYLPVNSN-WKRYLDTSNEIYEDLDIESKFLLSQQANQACQLmyndnykrdlwlwdqnwtskvlklkkekkkkpkitv 663  pea aphid
Feature 1                                                                                         
3IKM_A        443 asklpiegagapgdpmdqedlgpcseeeefqqdvmaraclqklkgttellpkrpqhlpghpgwyrklcprlddpawtpgp 522  human
Q27607        477 elkdsgntpeerrlqakfqhlydqqallparrpllpgyplwyrklcrkppakradeileddeepwspgaseistgmqiap 556  fruit fly
Q12704        466 vpkwykkaycktekravitaksrlapillrlkwkkhplaws--------------------------------------- 506  fission yeast
XP_001728845  610 ldasafvpawwrdrvanaktklsarvkivpqllqlqcdgnwvvtdgkrwamqcgegtvelpgsplsqavrkkhvitsggg 689  Malassezia gl...
EDK36807      455 kqafltgypewyrdlfrnkekemnisvrtritplllklkwegypllw--------------------------------- 501  Pichia guilli...
Q9Y767        488 palnqklpgypqwykdlfvkvpkelsgldepdkeqenrkarhefinltvrsriapl------------------------ 543  Neurospora cr...
P15801        459 lpgfpewyrqlfpskdtvepkitiksriipilfklswenspviws----------------------------------- 503  baker's yeast
Q01941        451 klpgypnwykqlivknelklttktrtsplllklawngnplywiqt----------------------------------- 495  Pichia pastoris
XP_505619     479 gerlpknvkfpgypewykalfkssagpmhittktritplllrlkwe---------------------------------- 524  Yarrowia lipo...
XP_001950479  664 enkpiepediyekrffelenmfkplmatserlplktphlagypewyrklcappkdphwvpgpllissgmhlvpkllslmw 743  pea aphid
Feature 1                                                                                         
3IKM_A        523 sllslqmrvtpklmaltwdgfplhyserhgwgylvpgrrdnlaklptgttlesagvvcpyraieslyrkhcleqgkqqlm 602  human
Q27607        557 kllslcwegyplhyer-----------------------------------------------eqgwgflvpfrsdsegv 589  fruit fly
Q12704            --------------------------------------------------------------------------------      fission yeast
XP_001728845  690 alaekalnavlissrdsdsimrelalmir----------------------dqghrdqpgltqldwtpvpyhdpaaqapw 747  Malassezia gl...
EDK36807          --------------------------------------------------------------------------------      Pichia guilli...
Q9Y767            --------------------------------------------------------------------------------      Neurospora cr...
P15801            --------------------------------------------------------------------------------      baker's yeast
Q01941            --------------------------------------------------------------------------------      Pichia pastoris
XP_505619         --------------------------------------------------------------------------------      Yarrowia lipo...
XP_001950479  744 kslplhy------------------------------------------------------------------vkgngwg 757  pea aphid
Feature 1                                                                                         
3IKM_A        603 pqeaglaeeflltdnsaiwqtveeldyleveaeakmenlraavpgqplaltarggpkdtqpsyhhgngpyndvdipgcwf 682  human
Q27607        590 drlpmeqllahcpvpefarlsaskaesdmafdmlpgqveqhlgkrehykklsqkqqrletqyqgsgvwcnkvlddccffl 669  fruit fly
Q12704        507 ---------------------------------------dtygwvfsvertskdeiemlldqglvpcsreedtkldynny 547  fission yeast
XP_001728845  748 wpkwywdlydaqaedvevtirtkiapillkiawdgapifrsrehgwvyrrthahpcdatpltfshaadtalsqgifyklp 827  Malassezia gl...
EDK36807      502 --------------------------------tdsagwcfkvpdetkevkrmaaknytlaklseedheslldelrdnghy 549  Pichia guilli...
Q9Y767        544 ------------------------llklswegyplfwsdqfgwtfqvprekaetfiqrqmtpvqfedpdvddrlrmdvdh 599  Neurospora cr...
P15801        504 ----------------------------------kesgwcfnvpheqvetykaknyvladsvsqeeeeirthnlglqctg 549  baker's yeast
Q01941        496 -----------------------------------qgwcfkvpknkteeyeklnfvmvslkklsedpgfesiraedlknf 540  Pichia pastoris
XP_505619     525 ----------------------------------gypvvwsdkegwmfrvpvseqahfeakkyklatldtephlrddgst 570  Yarrowia lipo...
XP_001950479  758 qlvpyetdiklpdaelvplkelkdhyiksnascdckikinntelhetvqtnlvkyecifkkknyktirnrpckenlaags 837  pea aphid
Feature 1                                                      #   #  ##                          
3IKM_A        683 fklphkdgnscnvgspfakdflpkmedgtlqagpgGASGPRALEINKMISFWRNAHKRISSQMVVWlprsalprav---i 759  human
Q27607        670 klphkngpsfrvgnplskdflnkfaenvlssgdpsCQAAARVIDIARMMSYWRNNRDRIMGQMVVWldsqqlpne----- 744  fruit fly
Q12704        548 iffkvphkdgpearcgsplsksyqryfeegilqsdYEVAKKALEMSASCSYWSSARDRIRSQMVVWdkdaelg------- 620  fission yeast
XP_001728845  828 hvngdgsnvgnpfskgflpyfengrlrslhpseqsAEAARAALEMNAQCSYWISARDRIEKQMVVWdgeadtcm------ 901  Malassezia gl...
EDK36807      550 qlfkiphpegpskrctsvlsksylryfengvlsseYEYAQDILRLNSEASYWMGNRNRILDQFVVYsdtsgsknmff--d 627  Pichia guilli...
Q9Y767        600 kyfklphkdgpnarcvnpmakgylpyfekgilsseYPYAKEALEMNASCSYWISARERIKNQMVVYedqlppsqrf---v 676  Neurospora cr...
P15801        550 vlfkvphpngptfnctnlltksynhffekgvlkseSELAHQALQINSSGSYWMSARERIQSQFVVPsckfpnefqslsak 629  baker's yeast
Q01941        541 tfvkvphpdgpsarvtncmtksclgffekgflnsqYPLAKDALQMAVASSYWTSSRERIMNQFVVFe------------- 607  Pichia pastoris
XP_505619     571 lcfriphkdggntrttqlmgksflghfekgtlssdNPQTKEMFEMSVCSSYWVSNRSRIMSQHCIWdgdgvd-------- 642  Yarrowia lipo...
XP_001950479  838 gmlklphkdgnhlnvgnplardflnkfsqnglsgkDSNAEHIIEISRMLSYWRNNRERVEGQIVVWtdk----------- 906  pea aphid
Feature 1                               ### # ####                               ##               
3IKM_A        760 rhpdydeegLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAH 839  human
Q27607        745 ftgekcqpiAYGAICPQVVACGTLTRRAMEPTWMTASNSRPDRLGSELRSMVQAPPGYRLVGADVDSQELWIASVLGDAY 824  fruit fly
Q12704        621 ---vpssvdGFGIILPCIIPMGTVTRRAVENTWLTASNSKKNRLGSELKAMIRAPDGYTFVGADVDSEELWIVALMGDSQ 697  fission yeast
XP_001728845  902 --gfddtqmRRGMILPQVITMGTVTRRAIEKTWLTASNAKKNRIGSELKSMVKASPGWSIVGADVDSEELWICSVMGDAQ 979  Malassezia gl...
EDK36807      628 tkvksrehpEMGIILPKLCSMGTITRRATENTWLTASNSKSNRIGSELKAMIEAPQGYAFVGADVDSEELWIASLVGDSM 707  Pichia guilli...
Q9Y767        677 nkdadsntpIGGFVLPQVIPMGTITRRAVERTWLTASNAKKNRVGSELKAMVRAPPGYVFVGADVDSEELWIASVVGDAT 756  Neurospora cr...
P15801        630 sslnnektnDLAIIIPKIVPMGTITRRAVENAWLTASNAKANRIGSELKTQVKAPPGYCFVGADVDSEELWIASLVGDSI 709  baker's yeast
Q01941        608 --------dDMGYILPQIIPMGTITRRAVENTWLTASNAKKNRLGSELKSLIEAPKGYCFVGADVDSEELWIASLIGDSV 679  Pichia pastoris
XP_505619     643 ----mgrgpGFGIIIPRIIPMGTITRRCVENTWLTASNAKKNRIGSELKSMIKAPPGYSFVGADVDSEELWIASLYGDSC 718  Yarrowia lipo...
XP_001950479  907 -------skGYGAIIPQVVVCGTLTRRAVERTWMTAANAIDERVGSELRSMIQSPPGYSLVGADVDSQELWIASVIGDSY 979  pea aphid
Feature 1                               #             #   #                                       
3IKM_A        840 FagmHGCTAFGWMTLQGRKSRGTDLHSKTAttVGISREHAKIFNYGRIYGagqpFAERLLMQFNHRLTqqEAAEKAQQMY 919  human
Q27607        825 AcgeHGATPLGWMTLSGSKSNGSDMHSITAkaVGISRDHAKVINYARIYGagqlFAETLLRQFNPTFSasEAKAKAMKMF 904  fruit fly
Q12704        698 Fr-lHGATALGMMTLEGKKSEGTDLHSKTAaiLGVSRDSAKVFNYGRLYGaglkHTTLLLMQMNPTLKtaEAKELAKKLY 776  fission yeast
XP_001728845  980 Fg-iHGATAIGWMTLEGSKAQGTDLHSKTAsiLGTSRDQAKVFNYSRIYGagirHAMQLLLKANPSMPvdEASRRAKQLY 1058 Malassezia gl...
EDK36807      708 Fk-iHGGTALGWMTLEGDKNEGTDLHSKTAeiLGISRNDAKVFNYGRIYGagvkFATTLLKQFNSELT--DAAALKVAQD 784  Pichia guilli...
Q9Y767        757 Fk-lHGGNAIGFMTLEGTKSQGTDLHSRTAsiLGITRNDAKVFNYGRIYGaglkFASQLLRQFNPSLTeaETTAIATKLY 835  Neurospora cr...
P15801        710 Fn-vHGGTAIGWMCLEGTKNEGTDLHTKTAqiLGCSRNEAKIFNYGRIYGagakFASQLLKRFNPSLT--DEETKKIANK 786  baker's yeast
Q01941        680 Fk-iHGGTAIGWMTLEGTKNEGTDLHSKTAkiLGISRNEAKIFNYGRIYG----AGIKFTTTLLKKFNpaLSDAEAKATA 754  Pichia pastoris
XP_505619     719 Fk-nHGSTAIGWMTLEGTKSEGTDLHSKTAsiLGISRNEAKIFNYGRIYG----AGLKFAEALLKQFSp-NVTDAEASTL 792  Yarrowia lipo...
XP_001950479  980 YgkeHGATAFGWMTLSGRKSDGTDMHSSTAkaIGITRDNAKVLNYARIYGagkpFSERLLKQFNPDLSpaQAKQKAIAMF 1059 pea aphid
Feature 1                                                                                         
3IKM_A        920 AATKGlrwy----------------------rlsdEGEWLVRELNLPVd---rTEGGWISLqdlrkvqretarksqwkkw 974  human
Q27607        905 SITKGkrvyrlreefhdeledrayssyeasrlaiqRNRTLAEVFHRPN-----WQGGTESAmfnrle------------- 966  fruit fly
Q12704        777 ASTKGv-----------------------------KSKMSKRLQEMGLpkltfWSQGTESFvfnkle------------- 814  fission yeast
XP_001728845 1059 AATKG------------------------------QNTRSQKYFGRRF-----WYGGTESFvfnkle------------- 1090 Malassezia gl...
EDK36807      785 LYARTk-----------------------------GQTGKSKFLDRPM-----YHGGTESVmfnale------------- 817  Pichia guilli...
Q9Y767        836 DATKG------------------------------AKTNRKSLYKRPF-----WRGGTESFvfnmle------------- 867  Neurospora cr...
P15801        787 LYENT------------------------------KGKTKRSKLFKKF-----WYGGSESIlfnkle------------- 818  baker's yeast
Q01941        755 NALYTa-----------------------------TKGISGRYDKKSI-----WYGGSESIifnrle------------- 787  Pichia pastoris
XP_505619     793 AGQLY------------------------------TSTKGKKIYSIGK-----YSGGTESIlfnkle------------- 824  Yarrowia lipo...
XP_001950479 1060 NMTKGnriyklhdtvlpevkkrehsrigaqelctiYNKSVDELFNKPI-----WSGGSESAmfnsle------------- 1121 pea aphid
Feature 1                                                                    #      #             
3IKM_A        975 evvaerawkggtesemfnklesiatsDIPRTPVLGCCISRALEPSAVQEEF------MTSRVNWVVQSSAVDYLHLMLVA 1048 human
Q27607        967 --------------------eiatgsQPRTPFLGGRLSRALEADTGPEQEQr----fLPTRINWVVQSGAVDFLHLMLVS 1022 fruit fly
Q12704        815 --------------------amaqlpSPRTPVLDAGITQALSSKNLSKNSF------MTSRVNWAIQSSAVDYLHLLLVS 868  fission yeast
XP_001728845 1091 --------------------eialseQPRTPALDCGITAALSKQFLPKTRGsaqqdyMPSRINWVVQSSGVDYLHLLITS 1150 Malassezia gl...
EDK36807      818 --------------------aiayqdDPRTPVLGAAITDALSKKNLNKNNY------MTSRINWAIQSSGVDYLHLLLIS 871  Pichia guilli...
Q9Y767        868 --------------------efaeqeRPRTPVLGAGITEALMSRWVSKGGF------LTSRINWAIQSSGVDYLHLLIIA 921  Neurospora cr...
P15801        819 --------------------siaeqeTPKTPVLGCGITYSLMKKNLRANSF------LPSRINWAIQSSGVDYLHLLCCS 872  baker's yeast
Q01941        788 --------------------aiaemaHPKTPVLGAGITAPLQKANLSTNNF------LTSRINWAIQSSGVDYLHLLIIS 841  Pichia pastoris
XP_505619     825 --------------------eiatqdMPETPVLGAVITKALSSQNLKKSSF------MTSRVNWTIQSSGVDYLHMLVVS 878  Yarrowia lipo...
XP_001950479 1122 --------------------qiacskQPKTPFLESRLSRALEMNGVDIDKF------IPTRINWVVQSGAVDFLHLMLVC 1175 pea aphid
Feature 1                          ###                                                            
3IKM_A       1049 MKWLfeefaIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLnDLPQSVAFFSAVDIDRCLRKEVTM 1128 human
Q27607       1023 MRWLm---gSHVRFCLSFHDELRYLVKEELSPKAALAMHITNLMTRSFCVSRIGLqDLPMSVAFFSSVEVDTVLRKECTM 1099 fruit fly
Q12704        869 MNHLikkyyLEARLSLTVHDEVRYLSSDKDKYRVAFALQVANLWTRAFFCQRLGInELPQSVAFFSSVDIDHVLRKDVKM 948  fission yeast
XP_001728845 1151 MTHLcktydIEARFMLSVHDEVRYLARDSDKYRAALALQIANLWTRSMFAFKLNMgDVPESCAFFAAVDIDHVLRKEVDD 1230 Malassezia gl...
EDK36807      872 MEYLiaryqVDARLILTVHDEIRYMVKEDQKYKLALLLQVSNLWTRAMFCEQMGLkEVPQSCAFFSEVDIDHVLRKEVTM 951  Pichia guilli...
Q9Y767        922 MDYLtrrfnLACRLAITVHDEIRYLAEEPDKYRVAMALQIANLWTRVMFAQQVGIqDLPQSCAFFSAVDIDHVLRKEVDM 1001 Neurospora cr...
P15801        873 MEYIikkynLEARLCISIHDEIRFLVSEKDKYRAAMALQISNIWTRAMFCQQMGInELPQNCAFFSQVDIDSVIRKEVNM 952  baker's yeast
Q01941        842 MDYLiklfdIDARLCITVHDEIRYLVKEEDKFRAAYALQISNLWTRAMFCQQLGInEVPQSCAFFSAVDLDFVLRKEVDL 921  Pichia pastoris
XP_505619     879 MEYLaakydIDMRLCITVHDELRFLVKNEDAYRAAMALQVSNIWTRGMFCQQSGIdDIPQGCAFFSAVDIDHVLRKEVDF 958  Yarrowia lipo...
XP_001950479 1176 MRWLi---hPNVRFCLSFHDEIRYLVPDEHRYQTALALHVTNLLVRAFCIKKLDMtDLPQSVAFFSSVEVDTALRKDALN 1252 pea aphid
Feature 1                 
3IKM_A       1129 DCKTPSNP 1136 human
Q27607       1100 DCKTPSNP 1107 fruit fly
Q12704        949 DCVTPSNK 956  fission yeast
XP_001728845 1231 PCVTPSQW 1238 Malassezia globosa CBS 7966
EDK36807      952 DCVTPSHP 959  Pichia guilliermondii ATCC 6260
Q9Y767       1002 DCITPSNP 1009 Neurospora crassa
P15801        953 DCITPSNK 960  baker's yeast
Q01941        922 DCVTPSNP 929  Pichia pastoris
XP_505619     959 DCITPTHP 966  Yarrowia lipolytica CLIB122
XP_001950479 1253 DCVTPSNP 1260 pea aphid

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