1L3V,3IKM,1TAQ,4BDP,3BDP,2KTQ,3KTQ


Conserved Protein Domain Family
DNA_pol_A

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cd06444: DNA_pol_A 
Click on image for an interactive view with Cn3D
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication
DNA polymerase family A, 5'-3' polymerase domain. 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 gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. 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.
Statistics
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PSSM-Id: 176473
View PSSM: cd06444
Aligned: 26 rows
Threshold Bit Score: 269.289
Threshold Setting Gi: 26988997
Created: 8-Jan-2008
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.
  • Structure:3KTQ; Thermus aquaticus DNA polymerase I binds DNA, two Mg ions, and ddCTP; contacts at 4.0A
    View structure with Cn3D
  • Citation:PMID 9857206

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                      
1L3V_A     200 DTKRLEQMGKELAEQLGTVEQRIYElagqefninspkqlgvilfeklql------------------------------- 248  Geobacillus stea...
1TAQ_A     452 DVAYLRALSLEVAEEIARLEAEVFRlaghpfnlnsrdqlervlfdelglp------------------------------ 501  Thermus aquaticus
4BDP_A     200 DTKRLEQMGKELAEQLGTVEQRIYElagqefninspkqlgvilfeklql------------------------------- 248  Geobacillus stea...
3BDP_A     200 DTKRLEQMGKELAEQLGTVEQRIYElagqefninspkqlgvilfeklql------------------------------- 248  Geobacillus stea...
2KTQ_A     158 DVAYLRALSLEVAEEIARLEAEVFRlaghpfnlnsrdqlervlfdelglp------------------------------ 207  Thermus aquaticus
3KTQ_A     160 DVAYLRALSLEVAEEIARLEAEVFRlaghpfnlnsrdqlervlfdelglp------------------------------ 209  Thermus aquaticus
XP_416549 2118 STAAYETQKQVMQAKLTEIETKAYQlaghsfsltspddvaevlflelklpqngdvkvqgnk------------------- 2178 chicken
NP_744422  223 NREKAALLYAKLAQRRGDLERELKEffkfwhapagevltkktrrvfiedprgnterrvklkgqpafnqvgwfekytegvr 302  Pseudomonas puti...
AAL58915   638 GWPSVGGDVLKELAGKVSAEYDFMDdvsdisleevvedddvetsetqkskt----------------------------- 688  thale cress
O67779     209 DVEELTNKLKAVERETQKRIQEFYIkyrvdplspkqlaslltkkfkl--------------------------------- 255  Aquifex aeolicus
Feature 1                                                                 #   #  ##            
1L3V_A     249 --------------------------pvlkktktgystsadvleklapyHEIVENILHYRQLGKLQSTYIEGLLKvvr-- 300  Geobacillus stea...
1TAQ_A     502 -------------------------aigktektgkrstsaavlealreaHPIVEKILQYRELTKLKSTYIDPLPDlih-- 554  Thermus aquaticus
4BDP_A     249 --------------------------pvlkktktgystsadvleklapyHEIVENILHYRQLGKLQSTYIEGLLKvvr-- 300  Geobacillus stea...
3BDP_A     249 --------------------------pvlkktktgystsadvleklapyHEIVENILHYRQLGKLQSTYIEGLLKvvr-- 300  Geobacillus stea...
2KTQ_A     208 -------------------------aigktektgkrstsaavlealreaHPIVEKILQYRELTKLKSTYIDPLPDlih-- 260  Thermus aquaticus
3KTQ_A     210 -------------------------aigktektgkrstsaavlealreaHPIVEKILQYRELTKLKSTYIDPLPDlih-- 262  Thermus aquaticus
XP_416549 2179 --------------ktlgytrrtsikgnrvrlskqfsttkdvleklkplHPLPGLILEWRRINSAISKVVFPLQRekrfn 2244 chicken
NP_744422  303 ytkvkivefnpssrdhiadrltalygwvpekftkggkpqvddevmsklsYPPCKLLTEYLLVAKRISQLAEGKQAwmlv- 381  Pseudomonas puti...
AAL58915   689 ------------------------ddetdtsaygtayvafgggergkeaCHAIASLCEVCSIDSLISNFILPLQGsnvs- 743  thale cress
O67779     256 ---------------------------nlpktpkgnvstddkaltsyqdVEPVKLVLEIRKLKKIADKLKELKEHlk--- 305  Aquifex aeolicus
Feature 1                      ### # ####                                                      
1L3V_A     301 --pdtKKVHTIFNQalTQTGRLSSTEPNLQNIPirl-------------------------------------------- 334  Geobacillus stea...
1TAQ_A     555 --prtGRLHTRFNQtaTATGRLCCCDPNLQNIPvrt-------------------------------------------- 588  Thermus aquaticus
4BDP_A     301 --pdtKKVHTIFNQalTQTGRLSSTEPNLQNIPirl-------------------------------------------- 334  Geobacillus stea...
3BDP_A     301 --pdtKKVHTIFNQalTQTGRLSSTEPNLQNIPirl-------------------------------------------- 334  Geobacillus stea...
2KTQ_A     261 --prtGRLHTRFNQtaTATGRLSSSDPNLQNIPvrt-------------------------------------------- 294  Thermus aquaticus
3KTQ_A     263 --prtGRLHTRFNQtaTATGRLSSSDPNLQNIPvrt-------------------------------------------- 296  Thermus aquaticus
XP_416549 2245 salgmERIYPVSQTh-TATGRVSFAEPNIQNVPrdfeiempivveesppfrthvyscavsrsllnferglgrkhssvlps 2323 chicken
NP_744422  382 --ekqGRIHGSVNPngAATGRATHAYPNVAQVPasgs------------------------------------------- 416  Pseudomonas puti...
AAL58915   744 --gkdGRVHCSLNIn-TETGRLSARRPNLQNQPale-------------------------------------------- 776  thale cress
O67779     306 ----nGRVYPEFKQigAVTGRMSSAHPNIQNIH----------------------------------------------- 334  Aquifex aeolicus
Feature 1                                           ##                             #           
1L3V_A     335 ---------------eegRKIRQAFVPSesdWLIFAADYSQIELRVLAHIAEDdnlmea--frrdlDIHTKTAMDIfqvs 397  Geobacillus stea...
1TAQ_A     589 ---------------plgQRIRRGFIAEe-gWLLVALDYSQIELRVLAHLSGDenlirv--fqegrDIHTETASWMfgvp 650  Thermus aquaticus
4BDP_A     335 ---------------eegRKIRQAFVPSesdWLIFAADYSQIELRVLAHIAEDdnlmea--frrdlDIHTKTAMDIfqvs 397  Geobacillus stea...
3BDP_A     335 ---------------eegRKIRQAFVPSesdWLIFAADYSQIELRVLAHIAEDdnlmea--frrdlDIHTKTAMDIfqvs 397  Geobacillus stea...
2KTQ_A     295 ---------------plgQRIRRAFIAEe-gWLLVALDYSQIELRVLAHLSGDenlirv--fqegrDIHTETASWMfgvp 356  Thermus aquaticus
3KTQ_A     297 ---------------plgQRIRRAFIAEe-gWLLVALDYSQIELRVLAHLSGDenlirv--fqegrDIHTETASWMfgvp 358  Thermus aquaticus
XP_416549 2324 gvntwtadrterrgipffVSMRHAFVPFp-gGFILAADYCQLELRILAHFSRDcrliea--fnkgaDVFKSIAAEWkmid 2400 chicken
NP_744422  417 ---------------pygKDCRELFTVPl-gWLLVGADASGLELRCLAHFMARydggkyvdillngDIHWANVQAMgits 480  Pseudomonas puti...
AAL58915   777 ---------------kdrYKIRKAFVASp-gNTLVVADYGQLELRILAHLTGCksmmea--fkaggDFHSRTAMNMyphv 838  thale cress
O67779     335 ------------------RDMRGIFKAEe-gNTFVISDFSQIELRIAAEYVKDplmlda--fkkgkDMHRYTASVVlgkk 393  Aquifex aeolicus
Feature 1                                        #   #                                         
1L3V_A     398 ed--------------------------evtpnMRRQAKAVNFGIVYGISDYGLAQnlnisrkeaaef------------ 439  Geobacillus stea...
1TAQ_A     651 re--------------------------avdplMRRAAKTINFGVLYGMSAHRLSQelaipyeeaqaf------------ 692  Thermus aquaticus
4BDP_A     398 ed--------------------------evtpnMRRQAKAVNFGIVYGISDYGLAQnlnisrkeaaef------------ 439  Geobacillus stea...
3BDP_A     398 ed--------------------------evtpnMRRQAKAVNFGIVYGISDYGLAQnlnisrkeaaef------------ 439  Geobacillus stea...
2KTQ_A     357 re--------------------------avdplMRRAAKTINFGVLYGMSAHRLSQelaipyeeaqaf------------ 398  Thermus aquaticus
3KTQ_A     359 re--------------------------avdplMRRAAKTINFGVLYGMSAHRLSQelaipyeeaqaf------------ 400  Thermus aquaticus
XP_416549 2401 se--------------------------avgdsTRQQAKQICYGIIYGIGAKSLGEqmgiddnkaany------------ 2442 chicken
NP_744422  481 ekrd---------------------dhntlhklYRDGAKTFIYAFLYGAGDEKVGTivfgmvakakalgldyqhlldvff 539  Pseudomonas puti...
AAL58915   839 reavengqvilewhpepgedkppvpllkdafgsERRKAKMLNFSIAYGKTAVGLSRdwkvstkeaqet------------ 906  thale cress
O67779     394 ee--------------------------eitkeERQLAKAINFGLIYGISAKGLAEyaklgygveisleea--------- 438  Aquifex aeolicus
Feature 1                                                                                #     
1L3V_A     440 ------------------ieryfesfpgvKRYMENIVQEAKqk--gYVTTLLHRrrylpditsrnfnvrsfaERMAMNTP 499  Geobacillus stea...
1TAQ_A     693 ------------------ieryfqsfpkvRAWIEKTLEEGRrr--gYVETLFGRrryvpdlearvksvreaaERMAFNMP 752  Thermus aquaticus
4BDP_A     440 ------------------ieryfesfpgvKRYMENIVQEAKqk--gYVTTLLHRrrylpditsrnfnvrsfaERMAMNTP 499  Geobacillus stea...
3BDP_A     440 ------------------ieryfesfpgvKRYMENIVQEAKqk--gYVTTLLHRrrylpditsrnfnvrsfaERMAMNTP 499  Geobacillus stea...
2KTQ_A     399 ------------------ieryfqsfpkvRAWIEKTLEEGRrr--gYVETLFGRrryvpdlearvksvreaaERMAFNMP 458  Thermus aquaticus
3KTQ_A     401 ------------------ieryfqsfpkvRAWIEKTLEEGRrr--gYVETLFGRrryvpdlearvksvreaaERMAFNMP 460  Thermus aquaticus
XP_416549 2443 ------------------iesfksrytgiQKFLKETVSNCRrd--gFVQTILGRrrylpairdsnpyikahaERQAVNTT 2502 chicken
NP_744422  540 ngqdnpdeealkaagkklkatflrktpalKKLVKAVKEAAKr---gHLVGLDGRhvh------------vksAHAALNYL 604  Pseudomonas puti...
AAL58915   907 ------------------vdlwyndrqevRKWQEMRKKEAIed--gYVLTLLGRsrrfpask--sraqrnhiQRAAINTP 964  thale cress
O67779     439 ---------------qvlrerffknfkafKEWHDRVKKELKekgevKGHTLLGRrfs------------antFNDAVNYP 491  Aquifex aeolicus
Feature 1       #                                                               ###            
1L3V_A     500 IQGSAADIIKKAMIDLNARlkee---------------------------------rlqaHLLLQVHDELILEAPkeemE 546  Geobacillus stea...
1TAQ_A     753 VQGTAADLMKLAMVKLFPRlee-----------------------------------mgaRMLLQVHDELVLEAPkeraE 797  Thermus aquaticus
4BDP_A     500 IQGSAADIIKKAMIDLNARlkee---------------------------------rlqaHLLLQVHDELILEAPkeemE 546  Geobacillus stea...
3BDP_A     500 IQGSAADIIKKAMIDLNARlkee---------------------------------rlqaHLLLQVHDELILEAPkeemE 546  Geobacillus stea...
2KTQ_A     459 VQGTAADLMKLAMVKLFPRlee-----------------------------------mgaRMLLQVHDELVLEAPkeraE 503  Thermus aquaticus
3KTQ_A     461 VQGTAADLMKLAMVKLFPRlee-----------------------------------mgaRMLLQVHDELVLEAPkeraE 505  Thermus aquaticus
XP_416549 2503 VQGSAADIVKTATVNIQRRlealssvnkshghlensfqrdktgrlsrkrnremlhpisggFFILQLHDELLYEVAeddvI 2582 chicken
NP_744422  605 LQGAGALACKQWLVFLDDElqarglk---------------------------hgwdgdyAFCAWVHDEVQIACRn---E 654  Pseudomonas puti...
AAL58915   965 VQGSAADVAMCAMLEISINqqlk---------------------------------klgwRLLLQIHDEVILEGPiesaE 1011 thale cress
O67779     492 IQGTGADLLKLAVLLFDANlqkk---------------------------------gidaKLVNLVHDEIVVECEkekaE 538  Aquifex aeolicus
Feature 1                                            
1L3V_A     547 RLCRLVPEVMEqav-------tlrVPLKVDYHYGSTWY 577  Geobacillus stearothermophilus
1TAQ_A     798 AVARLAKEVMEgvy-------plaVPLEVEVGIGEDWL 828  Thermus aquaticus
4BDP_A     547 RLCRLVPEVMEqav-------tlrVPLKVDYHYGSTWY 577  Geobacillus stearothermophilus
3BDP_A     547 RLCRLVPEVMEqav-------tlrVPLKVDYHYGSTWY 577  Geobacillus stearothermophilus
2KTQ_A     504 AVARLAKEVMEgvy-------plaVPLEVEVGIGEDWL 534  Thermus aquaticus
3KTQ_A     506 AVARLAKEVMEgvy-------plaVPLEVEVGIGEDWL 536  Thermus aquaticus
XP_416549 2583 QVAQIVKHEMEnav-------klsVKLNVKVKIGPSWG 2613 chicken
NP_744422  655 AIAVIVREAAEacvakageafnfrCPLAGESKMGLNWA 692  Pseudomonas putida KT2440
AAL58915  1012 IAKDIVVDCMSkpfng---rnilsVDLSVDAKCAQNWY 1046 thale cress
O67779     539 EVKEILEKSMKtagki----ilkeVPVEVESVINERWT 572  Aquifex aeolicus

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