DPO1_ECOLI
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 03-AUG-2022, entry version 213.
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; Proteobacteria; 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}.
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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 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 AlphaFoldDB; P00582; -.
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 SWISS-2DPAGE; P00582; -.
DR jPOST; P00582; -.
DR PaxDb; P00582; -.
DR PRIDE; P00582; -.
DR EnsemblBacteria; AAC76861; AAC76861; b3863.
DR EnsemblBacteria; BAE77445; BAE77445; BAE77445.
DR GeneID; 66672231; -.
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 PhylomeDB; P00582; -.
DR BioCyc; EcoCyc:EG10746-MON; -.
DR BioCyc; MetaCyc:EG10746-MON; -.
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; cd09898; H3TH_53EXO; 1.
DR Gene3D; 3.30.420.10; -; 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 PANTHER; PTHR10133; PTHR10133; 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; SSF47807; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
DR TIGRFAMs; TIGR00593; pola; 1.
DR PROSITE; PS00447; DNA_POLYMERASE_A; 1.
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
