ID DPO1_ECOLI Reviewed; 928 AA. AC P00582; Q2M8G1; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 21-JUL-1986, sequence version 1. DT 27-MAR-2024, entry version 221. DE RecName: Full=DNA polymerase I; DE Short=POL I; DE EC=2.7.7.7; GN Name=polA; Synonyms=resA; OrderedLocusNames=b3863, JW3835; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RX PubMed=6276402; DOI=10.1016/s0021-9258(19)68132-9; RA Joyce C.M., Kelley W.S., Grindley N.D.F.; RT "Nucleotide sequence of the Escherichia coli polA gene and primary RT structure of DNA polymerase I."; RL J. Biol. Chem. 257:1958-1964(1982). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=8346018; DOI=10.1093/nar/21.15.3391; RA Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.; RT "Analysis of the Escherichia coli genome. III. DNA sequence of the region RT from 87.2 to 89.2 minutes."; RL Nucleic Acids Res. 21:3391-3398(1993). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=9278503; DOI=10.1126/science.277.5331.1453; RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., RA Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1462(1997). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=16738553; DOI=10.1038/msb4100049; RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.; RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 RT and W3110."; RL Mol. Syst. Biol. 2:E1-E5(2006). RN [5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 918-928. RC STRAIN=K12; RX PubMed=6183253; DOI=10.1128/jb.152.3.1211-1219.1982; RA Joyce C.M., Grindley N.D.; RT "Identification of two genes immediately downstream from the polA gene of RT Escherichia coli."; RL J. Bacteriol. 152:1211-1219(1982). RN [6] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 284-350. RX PubMed=6302278; DOI=10.1016/0022-2836(83)90049-9; RA Kelley W.S., Joyce C.M.; RT "Genetic characterization of early amber mutations in the Escherichia coli RT polA gene and purification of the amber peptides."; RL J. Mol. Biol. 164:529-560(1983). RN [7] RP AMINO-ACID COMPOSITION, AND PARTIAL PROTEIN SEQUENCE. RX PubMed=7035456; DOI=10.1016/s0021-9258(19)68133-0; RA Brown W.E., Stump K.H., Kelley W.S.; RT "Escherichia coli DNA polymerase I. Sequence characterization and secondary RT structure prediction."; RL J. Biol. Chem. 257:1965-1972(1982). RN [8] RP IDENTIFICATION BY 2D-GEL. RX PubMed=9298644; DOI=10.1002/elps.1150180805; RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.; RT "Escherichia coli proteome analysis using the gene-protein database."; RL Electrophoresis 18:1243-1251(1997). RN [9] RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=3883192; DOI=10.1038/313762a0; RA Ollis D.L., Brick P., Hamlin R., Xuong N.G., Steitz T.A.; RT "Structure of large fragment of Escherichia coli DNA polymerase I complexed RT with dTMP."; RL Nature 313:762-766(1985). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=1989886; DOI=10.1002/j.1460-2075.1991.tb07917.x; RA Beese L.S., Steitz T.A.; RT "Structural basis for the 3'-5' exonuclease activity of Escherichia coli RT DNA polymerase I: a two metal ion mechanism."; RL EMBO J. 10:25-33(1991). RN [11] RP X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=8469987; DOI=10.1126/science.8469987; RA Beese L.S., Derbyshire V., Steitz T.A.; RT "Structure of DNA polymerase I Klenow fragment bound to duplex DNA."; RL Science 260:352-355(1993). RN [12] RP X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=8260491; DOI=10.1021/bi00214a004; RA Beese L.S., Friedman J.M., Steitz T.A.; RT "Crystal structures of the Klenow fragment of DNA polymerase I complexed RT with deoxynucleoside triphosphate and pyrophosphate."; RL Biochemistry 32:14095-14101(1993). RN [13] RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=9514742; DOI=10.1006/jmbi.1997.1586; RA Brautigam C.A., Steitz T.A.; RT "Structural principles for the inhibition of the 3'-5' exonuclease activity RT of Escherichia coli DNA polymerase I by phosphorothioates."; RL J. Mol. Biol. 277:363-377(1998). RN [14] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=9888810; DOI=10.1021/bi981537g; RA Brautigam C.A., Sun S., Piccirilli J.A., Steitz T.A.; RT "Structures of normal single-stranded DNA and deoxyribo-3'-S- RT phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA RT polymerase I from Escherichia coli."; RL Biochemistry 38:696-704(1999). RN [15] RP X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF KLENOW FRAGMENT. RX PubMed=10588690; DOI=10.1073/pnas.96.25.14240; RA Teplova M., Wallace S.T., Tereshko V., Minasov G., Symons A.M., Cook P.D., RA Manoharan M., Egli M.; RT "Structural origins of the exonuclease resistance of a zwitterionic RNA."; RL Proc. Natl. Acad. Sci. U.S.A. 96:14240-14245(1999). RN [16] RP STRUCTURE BY NMR OF 728-777. RX PubMed=8442659; DOI=10.1006/abbi.1993.1130; RA Mullen G.P., Vaughn J.B. Jr., Mildvan A.S.; RT "Sequential proton NMR resonance assignments, circular dichroism, and RT structural properties of a 50-residue substrate-binding peptide from DNA RT polymerase I."; RL Arch. Biochem. Biophys. 301:174-183(1993). CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase CC exhibits 3'-5' and 5'-3' exonuclease activity. It is able to utilize CC nicked circular duplex DNA as a template and can unwind the parental CC DNA strand from its template. CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, CC ChEBI:CHEBI:173112; EC=2.7.7.7; CC -!- SUBUNIT: Single-chain monomer with multiple functions. CC -!- SIMILARITY: Belongs to the DNA polymerase type-A family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; V00317; CAA23607.1; -; Genomic_DNA. DR EMBL; L19201; AAB02998.1; -; Genomic_DNA. DR EMBL; U00096; AAC76861.1; -; Genomic_DNA. DR EMBL; AP009048; BAE77445.1; -; Genomic_DNA. DR EMBL; J01663; AAA24402.1; -; Genomic_DNA. DR EMBL; J01664; AAA24404.1; -; Genomic_DNA. DR PIR; A92360; DJECI. DR RefSeq; NP_418300.1; NC_000913.3. DR RefSeq; WP_000250006.1; NZ_SSZK01000026.1. DR PDB; 1D8Y; X-ray; 2.08 A; A=324-928. DR PDB; 1D9D; X-ray; 2.18 A; A=324-928. DR PDB; 1D9F; X-ray; 3.00 A; A=324-928. DR PDB; 1DPI; X-ray; 2.80 A; A=324-928. DR PDB; 1KFD; X-ray; 3.90 A; A=324-928. DR PDB; 1KFS; X-ray; 2.10 A; A=324-928. DR PDB; 1KLN; X-ray; 3.20 A; A=324-928. DR PDB; 1KRP; X-ray; 2.20 A; A=324-928. DR PDB; 1KSP; X-ray; 2.30 A; A=324-928. DR PDB; 1QSL; X-ray; 2.20 A; A=324-928. DR PDB; 2KFN; X-ray; 2.03 A; A=324-928. DR PDB; 2KFZ; X-ray; 2.03 A; A=324-928. DR PDB; 2KZM; X-ray; 2.60 A; A=324-928. DR PDB; 2KZZ; X-ray; 2.25 A; A=324-928. DR PDB; 8OO6; EM; 4.30 A; A=328-928. DR PDB; 8OOY; EM; 4.00 A; A=328-928. DR PDBsum; 1D8Y; -. DR PDBsum; 1D9D; -. DR PDBsum; 1D9F; -. DR PDBsum; 1DPI; -. DR PDBsum; 1KFD; -. DR PDBsum; 1KFS; -. DR PDBsum; 1KLN; -. DR PDBsum; 1KRP; -. DR PDBsum; 1KSP; -. DR PDBsum; 1QSL; -. DR PDBsum; 2KFN; -. DR PDBsum; 2KFZ; -. DR PDBsum; 2KZM; -. DR PDBsum; 2KZZ; -. DR PDBsum; 8OO6; -. DR PDBsum; 8OOY; -. DR AlphaFoldDB; P00582; -. DR EMDB; EMD-17005; -. DR EMDB; EMD-17033; -. DR SMR; P00582; -. DR BioGRID; 4262182; 125. DR DIP; DIP-10524N; -. DR IntAct; P00582; 33. DR STRING; 511145.b3863; -. DR BindingDB; P00582; -. DR ChEMBL; CHEMBL4298; -. DR DrugBank; DB00548; Azelaic acid. DR DrugBank; DB08432; THYMIDINE-5'-THIOPHOSPHATE. DR jPOST; P00582; -. DR PaxDb; 511145-b3863; -. DR EnsemblBacteria; AAC76861; AAC76861; b3863. DR GeneID; 75174097; -. DR GeneID; 948356; -. DR KEGG; ecj:JW3835; -. DR KEGG; eco:b3863; -. DR PATRIC; fig|1411691.4.peg.2851; -. DR EchoBASE; EB0739; -. DR eggNOG; COG0258; Bacteria. DR eggNOG; COG0749; Bacteria. DR HOGENOM; CLU_004675_0_1_6; -. DR InParanoid; P00582; -. DR OMA; NRPPMPD; -. DR OrthoDB; 9806424at2; -. DR PhylomeDB; P00582; -. DR BioCyc; EcoCyc:EG10746-MONOMER; -. DR BioCyc; MetaCyc:EG10746-MONOMER; -. DR BRENDA; 2.7.7.7; 2026. DR SABIO-RK; P00582; -. DR EvolutionaryTrace; P00582; -. DR PRO; PR:P00582; -. DR Proteomes; UP000000318; Chromosome. DR Proteomes; UP000000625; Chromosome. DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc. DR GO; GO:0005829; C:cytosol; IDA:EcoCyc. DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:EcoCyc. DR GO; GO:0008409; F:5'-3' exonuclease activity; IDA:EcoCyc. DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc. DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:EcoCyc. DR GO; GO:0006284; P:base-excision repair; IDA:EcoCyc. DR GO; GO:0006281; P:DNA repair; IMP:EcoCyc. DR GO; GO:0006260; P:DNA replication; IDA:EcoCyc. DR GO; GO:0006261; P:DNA-templated DNA replication; IDA:EcoCyc. DR GO; GO:0006302; P:double-strand break repair; IBA:GO_Central. DR CDD; cd08637; DNA_pol_A_pol_I_C; 1. DR CDD; cd06139; DNA_polA_I_Ecoli_like_exo; 1. DR CDD; cd09898; H3TH_53EXO; 1. DR CDD; cd09859; PIN_53EXO; 1. DR Gene3D; 3.30.70.370; -; 1. DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2. DR Gene3D; 3.40.50.1010; 5'-nuclease; 1. DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1. DR InterPro; IPR002562; 3'-5'_exonuclease_dom. DR InterPro; IPR020046; 5-3_exonucl_a-hlix_arch_N. DR InterPro; IPR002421; 5-3_exonuclease. DR InterPro; IPR036279; 5-3_exonuclease_C_sf. DR InterPro; IPR019760; DNA-dir_DNA_pol_A_CS. DR InterPro; IPR001098; DNA-dir_DNA_pol_A_palm_dom. DR InterPro; IPR043502; DNA/RNA_pol_sf. DR InterPro; IPR020045; DNA_polI_H3TH. DR InterPro; IPR018320; DNA_polymerase_1. DR InterPro; IPR002298; DNA_polymerase_A. DR InterPro; IPR008918; HhH2. DR InterPro; IPR029060; PIN-like_dom_sf. DR InterPro; IPR012337; RNaseH-like_sf. DR InterPro; IPR036397; RNaseH_sf. DR NCBIfam; TIGR00593; pola; 1. DR PANTHER; PTHR10133; DNA POLYMERASE I; 1. DR PANTHER; PTHR10133:SF62; DNA POLYMERASE THETA; 1. DR Pfam; PF01367; 5_3_exonuc; 1. DR Pfam; PF02739; 5_3_exonuc_N; 1. DR Pfam; PF00476; DNA_pol_A; 1. DR Pfam; PF01612; DNA_pol_A_exo1; 1. DR PRINTS; PR00868; DNAPOLI. DR SMART; SM00474; 35EXOc; 1. DR SMART; SM00475; 53EXOc; 1. DR SMART; SM00279; HhH2; 1. DR SMART; SM00482; POLAc; 1. DR SUPFAM; SSF47807; 5' to 3' exonuclease, C-terminal subdomain; 1. DR SUPFAM; SSF56672; DNA/RNA polymerases; 1. DR SUPFAM; SSF88723; PIN domain-like; 1. DR SUPFAM; SSF53098; Ribonuclease H-like; 1. DR PROSITE; PS00447; DNA_POLYMERASE_A; 1. DR SWISS-2DPAGE; P00582; -. PE 1: Evidence at protein level; KW 3D-structure; Direct protein sequencing; DNA damage; DNA repair; KW DNA replication; DNA-binding; DNA-directed DNA polymerase; Exonuclease; KW Hydrolase; Nuclease; Nucleotidyltransferase; Reference proteome; KW Transferase. FT CHAIN 1..928 FT /note="DNA polymerase I" FT /id="PRO_0000101239" FT DOMAIN 1..323 FT /note="5'-3' exonuclease" FT DOMAIN 324..517 FT /note="3'-5' exonuclease" FT REGION 324..928 FT /note="Klenow fragment" FT REGION 521..928 FT /note="Polymerase" FT STRAND 327..332 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 336..347 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 349..359 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 363..365 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 368..376 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 379..384 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 398..409 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 416..420 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 421..429 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 430..432 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 438..441 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 442..449 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 451..453 FT /evidence="ECO:0007829|PDB:1KSP" FT HELIX 458..465 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 473..477 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 480..482 FT /evidence="ECO:0007829|PDB:1KFS" FT HELIX 486..488 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 491..515 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 520..528 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 530..543 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 545..547 FT /evidence="ECO:0007829|PDB:1KLN" FT HELIX 549..573 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 574..576 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 582..585 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 587..590 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 591..593 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 608..610 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 613..617 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 618..620 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 623..639 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 640..643 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 644..647 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 650..652 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 653..655 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 658..662 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 665..667 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 670..674 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 676..678 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 681..683 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 684..691 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 699..706 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 709..717 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 721..728 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 733..741 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 746..748 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 751..765 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 772..777 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 781..783 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 784..794 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 796..812 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 813..816 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 822..824 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 826..829 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 833..870 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 873..880 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 883..889 FT /evidence="ECO:0007829|PDB:2KFN" FT TURN 890..892 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 893..906 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 910..912 FT /evidence="ECO:0007829|PDB:2KFN" FT STRAND 916..923 FT /evidence="ECO:0007829|PDB:2KFN" FT HELIX 924..927 FT /evidence="ECO:0007829|PDB:2KFN" SQ SEQUENCE 928 AA; 103118 MW; DAAE1C448A59030C CRC64; MVQIPQNPLI LVDGSSYLYR AYHAFPPLTN SAGEPTGAMY GVLNMLRSLI MQYKPTHAAV VFDAKGKTFR DELFEHYKSH RPPMPDDLRA QIEPLHAMVK AMGLPLLAVS GVEADDVIGT LAREAEKAGR PVLISTGDKD MAQLVTPNIT LINTMTNTIL GPEEVVNKYG VPPELIIDFL ALMGDSSDNI PGVPGVGEKT AQALLQGLGG LDTLYAEPEK IAGLSFRGAK TMAAKLEQNK EVAYLSYQLA TIKTDVELEL TCEQLEVQQP AAEELLGLFK KYEFKRWTAD VEAGKWLQAK GAKPAAKPQE TSVADEAPEV TATVISYDNY VTILDEETLK AWIAKLEKAP VFAFDTETDS LDNISANLVG LSFAIEPGVA AYIPVAHDYL DAPDQISRER ALELLKPLLE DEKALKVGQN LKYDRGILAN YGIELRGIAF DTMLESYILN SVAGRHDMDS LAERWLKHKT ITFEEIAGKG KNQLTFNQIA LEEAGRYAAE DADVTLQLHL KMWPDLQKHK GPLNVFENIE MPLVPVLSRI ERNGVKIDPK VLHNHSEELT LRLAELEKKA HEIAGEEFNL SSTKQLQTIL FEKQGIKPLK KTPGGAPSTS EEVLEELALD YPLPKVILEY RGLAKLKSTY TDKLPLMINP KTGRVHTSYH QAVTATGRLS STDPNLQNIP VRNEEGRRIR QAFIAPEDYV IVSADYSQIE LRIMAHLSRD KGLLTAFAEG KDIHRATAAE VFGLPLETVT SEQRRSAKAI NFGLIYGMSA FGLARQLNIP RKEAQKYMDL YFERYPGVLE YMERTRAQAK EQGYVETLDG RRLYLPDIKS SNGARRAAAE RAAINAPMQG TAADIIKRAM IAVDAWLQAE QPRVRMIMQV HDELVFEVHK DDVDAVAKQI HQLMENCTRL DVPLLVEVGS GENWDQAH //