Conserved Protein Domain Family
DNA_pol_A_theta

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cd08638: DNA_pol_A_theta 
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). 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 functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. Polymerase theta mostly has amino-terminal helicase domain, a carboxy-terminal polymerase domain and an intervening space region.
Statistics
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PSSM-Id: 176475
View PSSM: cd08638
Aligned: 39 rows
Threshold Bit Score: 324.179
Threshold Setting Gi: 294948800
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                                                                                         
XP_416549    2114 GIGFSTAAYETQKQVMQAKLTEIETKAYQlaghsfsltspddvaevlflelklpqngdvkvqgnkktlgytrrtsikgnr 2193 chicken
XP_001701481 2014 GIALAPQVLKDQRGPLEARLRQLAAKAHLaagmtfdlnspkdvsevlfq-------------------hlnlppppcafs 2074 Chlamydomonas...
XP_001785063 1257 SLGLDMRVCRKAQSHLHCKLRELEAQGEKlagmsfslsapaevahvl----------------------yrhlklpvppg 1314 Physcomitrell...
EEH60606     1521 GVAFAPATLSRQLRRATKRVREIETEAVAvvathfacrhpgmappefnlassddvar---vlfdappaglgaepprgakp 1597 Micromonas pu...
XP_002507779 1498 GVAFDPSVLCRQMRQANRRLREIEREADAlvskqvpgaepafslassadvarv----------lfenlklppppcavvqc 1567 Micromonas sp...
NP_001078482 1724 GIGIDIEGCLRARNILRDKLRSLEKKAFElagmtfslhnpadianvlf---------------------gqlklpipenq 1782 thale cress
CAL55548     1032 KVPFDPRRLKEEIAAMDDRLKKLEEYAKKqkwldplhpanlrraftdnaylvkclyehlkltppagselaftkdwvsnak 1111 Ostreococcus ...
Q7Z5Q5        442 AIQVNKEEMEKTSALLGARLKELEQEAHFvagerflitsnnqlreilfgk----------------lklhllsqrnslpr 505  human
NP_001093496  722 KMHVDKEALKKTSEMLGSKLKQLEQEAHQaagqkflvsssaqlrlilfek-----------------lrlhelcenkklp 784  zebrafish
XP_002516582 1718 GIGVDMEACLRARNVLGKKLRHLEKKAYElagmtfslytaadianvly---------------------grlklpipegh 1776 castor bean
Feature 1                                            #   #  ##                                    
XP_416549    2194 vrlskqfSTTKDVLEKLkp-----lHPLPGLILEWRRINSAISKVVFPLQRekrf------------------------- 2243 chicken
XP_001701481 2075 nqnqrhpSTKKEVLEELees---thHPIIRLLLDYRTLHKLLTGFVETLYHtakgqwqrqqhelercqgqgqqpqrggaa 2151 Chlamydomonas...
XP_001785063 1315 ckgkhhpSTDKQALEFLrn-----hHPIADIIKEHRSLSKLLQSTLGSIIAwakspeplf-------------------- 1369 Physcomitrell...
EEH60606     1598 taargrrSTRQDDLLALvreqggpiAAFPKLVLEHRSLRKLLDEANEFGRLakselggd--------------------- 1656 Micromonas pu...
XP_002507779 1568 gngrrrlRANAEVLAALkd-----qSDLPALVLEHRTLSRCVAMADEMVELalggarrd--------------------- 1621 Micromonas sp...
NP_001078482 1783 skgklhpSTDKHCLDLLrn-----eHPVVPIIKEHRTLAKLLNCTLGSICSlakl------------------------- 1832 thale cress
CAL55548     1112 ectvstkTTYEKVHEQSg-------HMFPLLILEHRSVFKRLTFADVLLGMyg--------------------------- 1157 Ostreococcus ...
Q7Z5Q5        506 tglqkypSTSEAVLNALrd-----lHPLPKIILEYRQVHKIKSTFVDGLLAc---------------------------- 552  human
NP_001093496  785 ktvkqqqSTSETALLQLqk-----lHPLPKIILEYRQIHKIKTTFVDGILSc---------------------------- 831  zebrafish
XP_002516582 1777 gkgklhpSTDKHCLDLLr------kKYCCFAFMFYATIAALKLGLLMLFFLi---------------------------- 1822 castor bean
Feature 1                                      ### # ####                                         
XP_416549    2244 ----------nsalGMERIYPVSQTH---TATGRVSFAEPNIQNVPrdfeiempivveesppfrthvyscavsrsllnfe 2310 chicken
XP_001701481 2152 tggavkpggpgpvpDVIRLCGTWLHTs--TATGRLAMDEPNLQTVPrpveytfmasqlsqasagtppaagad-------- 2221 Chlamydomonas...
XP_001785063 1370 -----ssqerssrgEIFSIAGHWLQTs--TATGRLSMEDPNLQCVEhavsftieggrsl--------------------- 1421 Physcomitrell...
EEH60606     1657 ------aaaaadesVTIRLRGVIHQTn--TGTGRLAMEDPNLQCVPrprefalsrayperls------------------ 1710 Micromonas pu...
XP_002507779 1622 -------egnssrgKITRLRGAIHQTn--TETGRLAMEEPNLQTVPkprtfrmadaydgrpgiiapeg------------ 1680 Micromonas sp...
NP_001078482 1833 ----------rlstQRYTLHGRWLQTs--TATGRLSIEEPNLQSVEhevefkldkng----------------------- 1877 thale cress
CAL55548     1158 ------------esMDSRIRYSIHQTn--HDCGRLTHIEPNFHSMAhdmkcvda-------------------------- 1197 Ostreococcus ...
Q7Z5Q5        553 -------------mKKGSISSTWNQTg--TVTGRLSAKHPNIQGISkhpiqittpkn----------------------- 594  human
NP_001093496  832 -------------tRKTFISSTWNQTs--TVSGRLSAKHPNFQALPklplqiskkqy----------------------- 873  zebrafish
XP_002516582 1823 --------------LMILIWVSEIKVllrTNLGVMQCVEHMVEFKIsmdknggd-------------------------- 1862 castor bean
Feature 1                                                           ##                            
XP_416549    2311 rglgrkhssvlpsgvntwtadrterrgipffVSMRHAFVPFp-gGFILAADYCQLELRILAHFSRDCRLIEAFnk----- 2384 chicken
XP_001701481 2222 -----gaelkllpgeergggageggrsvtlhFNLRSAFVAPp-gYMVLAADYKQIELRLMAHFSSDAALCALLrn----- 2290 Chlamydomonas...
XP_001785063 1422 -------------------dgdqekannvveVNARQAFVPSqegWILLSADYSQIELRLMAHFSGDPSLVSLLsh----- 1477 Physcomitrell...
EEH60606     1711 ---------------asgrvspgtdagaeetLAIRNAFRAPr-gKKLIAFDYKQIELRVIAHLSCDRGLIAALcv----- 1769 Micromonas pu...
XP_002507779 1681 ----------sakahktrepspgtevgseetLSVRNAFVAPp-gAVLLSADYRQLELRVMAHMSGDEGLVRAFnhegapp 1749 Micromonas sp...
NP_001078482 1878 --------------------rdvssdadrykINARDFFVPTqenWLLLTADYSQIELRLMAHFSRDSSLISKLsq----- 1932 thale cress
CAL55548     1198 -----------------------fdgldapvISVRSAFTPPa-dRVFLRVDYSHLELRVMAHFSGDQTLIALLqnpep-- 1251 Ostreococcus ...
Q7Z5Q5        595 ---------------------fkgkedkiltISPRAMFVSSk-gHTFLAADFSQIELRILTHLSGDPELLKLFqes---- 648  human
NP_001093496  874 ---------------------ihgkasdivtVHPRAMFIPRe-gWTFLSADFCQVELRLLAHLSADPQLLRIFqs----- 926  zebrafish
XP_002516582 1863 ------------------------aeannykINAREFFIPTqenWLLLTADYSQIELRLMAHFSKDASLIELLsk----- 1913 castor bean
Feature 1                #                     #   #                                              
XP_416549    2385 ---gADVFKSIAAEWkmidse--avgdsTRQQAKQICYGIIYGIGAKSLGEQMgiddnKAANYIESFksrYTGIQKFLKE 2459 chicken
XP_001701481 2291 --paQDPFILLAAEWkkvpve--qvtpeVRVQAKRLAYGMLYGMGTNTLAQELgvsvaEAGELSDNFrraIPSVDRWMRE 2366 Chlamydomonas...
XP_001785063 1478 --ptGDLFRVLAAQWtglpmc--evsdkQRERTKRLVYGILYGMGVNTLAEHLecpvaEAQVMLERFkgtFPLVTTWLSH 1553 Physcomitrell...
EEH60606     1770 --rsVDPFKVIAARWkgdgttpknvsdeDRAKAKELCYGICYGAGVGRYQQAMgvtelEARAAIEDFkrsLPGVERWKSA 1847 Micromonas pu...
XP_002507779 1750 hhpdADPFRFLASRWrgvevg--kvsdaDRAVAKQLAYGVLYGSGPARFAQEMgvtesEARVQIEAFkasVPGVERWRKK 1827 Micromonas sp...
NP_001078482 1933 --peGDVFTMIAAKWtgkaed--svsphDRDQTKRLIYGILYGMGANRLAEQLectsdEAKEKIRSFkssFPAVTSWLNE 2008 thale cress
CAL55548     1252 vnahDDPFTMLACKWrgvpln--avsvdERQRVKNLVYGILYGSGVKRLARELrlsdeKAKILVDELksmLPTLMNWRDD 1329 Ostreococcus ...
Q7Z5Q5        649 --erDDVFSTLTSQWkdvpve--qvthaDREQTKKVVYAVVYGAGKERLAACLgvpiqEAAQFLESFlqkYKKIKDFARA 724  human
NP_001093496  927 --peADAFTMLAAQWkgvsed--rvsleDREQAKRIVYSVVYGAGRERLSGILgvsaeEASRFQDSFlktYREVPAFIQH 1002 zebrafish
XP_002516582 1914 --phGDVFTIIAARWtgkaee--svaslERDQTKRLVYGILYGMGANTLAQQLecssdEAAEKIKSFkscFPGVASWLHE 1989 castor bean
Feature 1                                                               #      #                  
XP_416549    2460 TVSNCRr---dGFVQTILGRRRYLpairdsn--------------pyikahaERQAVNTTVQGSAADIVKTATVNIQRRl 2522 chicken
XP_001701481 2367 VVEAVRs---cGYTTTLMGRRRYYsrinerask----------darsaraqaERQAVNTVCQGSAADLIKAAMVTLQRRl 2433 Chlamydomonas...
XP_001785063 1554 AVDSCRq---kGYITTLSGRKRYLdkintgk--------------wgeqakaERQAVNSICQGSAADLIKLAMIKVHDAi 1616 Physcomitrell...
EEH60606     1848 LVKDARer-tpPHVRTIAGRCRFLpslnatga------------ggeiraadERKAINTACQGSAADIVKRVMIELHAKl 1914 Micromonas pu...
XP_002507779 1828 LIETASra-spPSVETICGRRRILsslapdaaltatgcedakrrfrldrsadERRAVNTACQGSAADVVKRAMIAVFDEl 1906 Micromonas sp...
NP_001078482 2009 TISFCQe---kGYIQTLKGRRRFLskikfgn--------------akekskaQRQAVNSMCQGSAADIIKIAMINIYSAi 2071 thale cress
CAL55548     1330 VVARAIeekpiPRVTTISSRHRYFpellsrs--------------gdersaaERQAVNTVCQGSAADIFKTAVVLVMETl 1395 Ostreococcus ...
Q7Z5Q5        725 AIAQCHq---tGCVVSIMGRRRPLprihahd--------------qqlraqaERQAVNFVVQGSAADLCKLAMIHVFTAv 787  human
NP_001093496 1003 TIQHCQs---hGFVRSIMGRRRFLphihsad--------------wslrnqaERQAVNFVLQGSAADLAKLAMIRICSQv 1065 zebrafish
XP_002516582 1990 AVASCRk---nGYVETLKGRKRFLskikfgn--------------skekskaQRQAVNSICQGSAADLIKIAMINIYSVi 2052 castor bean
Feature 1                                                      ###                                
XP_416549    2523 ealssvnkshghlensfqrdktgrlsrkrnremlhpisggFFILQLHDELLYEVAEddVIQVAQIVKHEMEnav------ 2596 chicken
XP_001701481 2434 eaeg-------------------------------laphvRMVLMVHDELVFEVAEqlLPAAARLVQAVLEgev------ 2476 Chlamydomonas...
XP_001785063 1617 sssh--------------------------------qgscRLLLQIHDELLLEVDKrvLKHVAQILRSSMEgai------ 1658 Physcomitrell...
EEH60606     1915 tsgggadddd-------------------ewaplrevdacEMVLQVHDELLFEVDErkVDVAVRAIRGVMErarev---- 1971 Micromonas pu...
XP_002507779 1907 dp-----------------------------------slaTPVLQIHDELLFEVDAsrVVEAARAVRAIMEragde---- 1947 Micromonas sp...
NP_001078482 2072 aedvdtaassss----------------setrfhmlkgrcRILLQVHDELVLEVDPsyVKLAAMLLQTSMEnav------ 2129 thale cress
CAL55548     1396 rakh-------------------------------lldrcQLVLTVHDEAVFEVNAsvAKAAARIVRNTMEsvagv---- 1440 Ostreococcus ...
Q7Z5Q5        788 aash--------------------------------tltaRLVAQIHDELLFEVEDpqIPECAALVRRTMEsleqvqale 835  human
NP_001093496 1066 ssd---------------------------------sqtaRLVAQIHDELLFEVEIsqLDQFAALVKKTMEslqhieyln 1112 zebrafish
XP_002516582 2053 arvdgpdpsss-----------------latkfhmlkgrcRILLQVHDELVLEVDPpvIKEAASLLQAGMEnaa------ 2109 castor bean
Feature 1                             
XP_416549    2597 -klsVKLNVKVKIGPSWGEL 2615 chicken
XP_001701481 2477 -alsVPLPVKLSAGPSWGQL 2495 Chlamydomonas reinhardtii
XP_001785063 1659 -tlrVPLRTKLQVGTSWGSL 1677 Physcomitrella patens subsp. patens
EEH60606     1972 hdmkVPLPVRVSVGDDWGRL 1991 Micromonas pusilla CCMP1545
XP_002507779 1948 fgftVPLPVKVSAGANWGDL 1967 Micromonas sp. RCC299
NP_001078482 2130 -sllVPLHVKLKVGKTWGSL 2148 thale cress
CAL55548     1441 fnlsVPLPVKAQIGPSLGDA 1460 Ostreococcus tauri
Q7Z5Q5        836 lqlqVPLKVSLSAGRSWGHL 855  human
NP_001093496 1113 vnlsVPLKVLLSTGRSWGSM 1132 zebrafish
XP_002516582 2110 --slLDMPGHVSGHTFLRER 2127 castor bean

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