DPO3E_ECOLI
ID DPO3E_ECOLI Reviewed; 243 AA.
AC P03007;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1988, sequence version 1.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=DNA polymerase III subunit epsilon;
DE EC=2.7.7.7;
GN Name=dnaQ; Synonyms=mutD; OrderedLocusNames=b0215, JW0205;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3023634; DOI=10.1016/0022-2836(86)90080-x;
RA Cox E.C., Horner D.L.;
RT "DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia
RT coli mutator gene.";
RL J. Mol. Biol. 190:113-117(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6316347; DOI=10.1073/pnas.80.23.7137;
RA Maki H., Horiuchi T., Sekiguchi M.;
RT "Structure and expression of the dnaQ mutator and the RNase H genes of
RT Escherichia coli: overlap of the promoter regions.";
RL Proc. Natl. Acad. Sci. U.S.A. 80:7137-7141(1983).
RN [3]
RP SEQUENCE REVISION.
RX PubMed=3540531; DOI=10.1007/bf02428026;
RA Takano K., Nakabeppu Y., Maki H., Horiuchi T., Sekiguchi M.;
RT "Structure and function of dnaQ and mutD mutators of Escherichia coli.";
RL Mol. Gen. Genet. 205:9-13(1986).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
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 [8]
RP FUNCTION AS THE EXONUCLEASE SUBUNIT.
RX PubMed=6340117; DOI=10.1073/pnas.80.8.2189;
RA Echols H., Lu C., Burgers P.M.;
RT "Mutator strains of Escherichia coli, mutD and dnaQ, with defective
RT exonucleolytic editing by DNA polymerase III holoenzyme.";
RL Proc. Natl. Acad. Sci. U.S.A. 80:2189-2192(1983).
RN [9]
RP REVIEW.
RX PubMed=1575709; DOI=10.1002/bies.950140206;
RA O'Donnell M.;
RT "Accessory protein function in the DNA polymerase III holoenzyme from E.
RT coli.";
RL Bioessays 14:105-111(1992).
RN [10]
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 [11]
RP REPLISOME COMPLEX, AND SUBUNIT.
RX PubMed=20413500; DOI=10.1126/science.1185757;
RA Reyes-Lamothe R., Sherratt D.J., Leake M.C.;
RT "Stoichiometry and architecture of active DNA replication machinery in
RT Escherichia coli.";
RL Science 328:498-501(2010).
RN [12]
RP REPLISOME COMPLEX, AND SUBUNIT.
RX PubMed=22157955; DOI=10.1038/nsmb.2179;
RA Georgescu R.E., Kurth I., O'Donnell M.E.;
RT "Single-molecule studies reveal the function of a third polymerase in the
RT replisome.";
RL Nat. Struct. Mol. Biol. 19:113-116(2011).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-186 IN COMPLEX WITH METAL IONS
RP AND SUBSTRATE ANALOG.
RX PubMed=11937058; DOI=10.1016/s0969-2126(02)00738-4;
RA Hamdan S., Carr P.D., Brown S.E., Ollis D.L., Dixon N.E.;
RT "Structural basis for proofreading during replication of the Escherichia
RT coli chromosome.";
RL Structure 10:535-546(2002).
RN [14] {ECO:0007744|PDB:5FKU, ECO:0007744|PDB:5FKV, ECO:0007744|PDB:5FKW}
RP STRUCTURE BY ELECTRON MICROSCOPY (7.30 ANGSTROMS) OF DNAE; DNAN; DNAQ; DNAX
RP WITH AND WITHOUT DNA, SUBUNIT, AND MUTAGENESIS OF 183-THR--PHE-187.
RX PubMed=26499492; DOI=10.7554/elife.11134;
RA Fernandez-Leiro R., Conrad J., Scheres S.H., Lamers M.H.;
RT "cryo-EM structures of the E. coli replicative DNA polymerase reveal its
RT dynamic interactions with the DNA sliding clamp, exonuclease and tau.";
RL Elife 4:0-0(2015).
CC -!- FUNCTION: DNA polymerase III is a complex, multichain enzyme
CC responsible for most of the replicative synthesis in bacteria. The
CC epsilon subunit contain the editing function and is a proofreading 3'-
CC 5' exonuclease (PubMed:6340117). Contacts both the beta sliding clamp
CC (dnaN) and the polymerase subunit (dnaE), stabilizing their interaction
CC (PubMed:26499492). {ECO:0000269|PubMed:26499492,
CC ECO:0000269|PubMed:6340117}.
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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Note=Binds 2 divalent metal cations. Magnesium or manganese.;
CC -!- SUBUNIT: In a ternary complex this subunit contacts both the beta
CC sliding clamp (dnaN) and the polymerase subunit (dnaE)
CC (PubMed:26499492). The DNA polymerase III holoenzyme complex contains
CC at least 10 different subunits organized into 3 functionally essential
CC subassemblies: the Pol III core, the beta sliding clamp processivity
CC factor and the clamp-loading complex. The Pol III core (subunits alpha,
CC epsilon and theta) contains the polymerase and the 3'-5' exonuclease
CC proofreading activities (PubMed:6340117). The polymerase is tethered to
CC the template via the dimeric beta sliding clamp processivity factor.
CC The clamp loader (also called gamma complex) assembles the beta sliding
CC clamp onto the primed template and plays a central role in the
CC organization and communication at the replication fork. The clamp-
CC loading complex contains delta, delta', psi and chi, and 3 copies of
CC either or both of two different DnaX proteins, gamma and tau. The DNA
CC replisome complex has a single clamp loader (3 tau and 1 each of delta,
CC delta', psi and chi subunits) which binds 3 Pol III cores (1 core on
CC the leading strand and 2 on the lagging strand) each with a beta
CC sliding clamp dimer. Additional proteins in the replisome are other
CC copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase
CC (PubMed:20413500, PubMed:22157955). {ECO:0000269|PubMed:11937058,
CC ECO:0000269|PubMed:20413500, ECO:0000269|PubMed:22157955,
CC ECO:0000269|PubMed:26499492, ECO:0000269|PubMed:6340117}.
CC -!- INTERACTION:
CC P03007; P10443: dnaE; NbExp=25; IntAct=EBI-549131, EBI-549111;
CC P03007; P0A988: dnaN; NbExp=6; IntAct=EBI-549131, EBI-542385;
CC P03007; P06710: dnaX; NbExp=6; IntAct=EBI-549131, EBI-549140;
CC P03007; P28630: holA; NbExp=3; IntAct=EBI-549131, EBI-549153;
CC P03007; P0ABS8: holE; NbExp=13; IntAct=EBI-549131, EBI-549182;
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB08637.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X04027; CAA27661.1; -; Genomic_DNA.
DR EMBL; K00985; AAA24564.1; -; Genomic_DNA.
DR EMBL; U70214; AAB08637.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC73320.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA77886.1; -; Genomic_DNA.
DR PIR; A64746; IQECQ.
DR RefSeq; NP_414751.1; NC_000913.3.
DR RefSeq; WP_001340895.1; NZ_SSZK01000029.1.
DR PDB; 1J53; X-ray; 1.80 A; A=1-186.
DR PDB; 1J54; X-ray; 1.70 A; A=1-186.
DR PDB; 2GUI; X-ray; 1.60 A; A=2-186.
DR PDB; 2IDO; X-ray; 2.10 A; A/C=1-186.
DR PDB; 2XY8; NMR; -; A=1-186.
DR PDB; 4GX8; X-ray; 1.70 A; A/B/C/D=209-243.
DR PDB; 4GX9; X-ray; 2.15 A; A/B/C/D=200-243.
DR PDB; 5FKU; EM; 8.34 A; D=1-243.
DR PDB; 5FKV; EM; 8.00 A; D=1-243.
DR PDB; 5FKW; EM; 7.30 A; D=1-243.
DR PDB; 5M1S; EM; 6.70 A; D=1-243.
DR PDBsum; 1J53; -.
DR PDBsum; 1J54; -.
DR PDBsum; 2GUI; -.
DR PDBsum; 2IDO; -.
DR PDBsum; 2XY8; -.
DR PDBsum; 4GX8; -.
DR PDBsum; 4GX9; -.
DR PDBsum; 5FKU; -.
DR PDBsum; 5FKV; -.
DR PDBsum; 5FKW; -.
DR PDBsum; 5M1S; -.
DR AlphaFoldDB; P03007; -.
DR BMRB; P03007; -.
DR SMR; P03007; -.
DR BioGRID; 4262121; 73.
DR BioGRID; 850796; 6.
DR ComplexPortal; CPX-1925; DNA polymerase III core complex.
DR DIP; DIP-9462N; -.
DR IntAct; P03007; 30.
DR MINT; P03007; -.
DR STRING; 511145.b0215; -.
DR ChEMBL; CHEMBL1075047; -.
DR DrugBank; DB01643; Thymidine monophosphate.
DR SWISS-2DPAGE; P03007; -.
DR jPOST; P03007; -.
DR PaxDb; P03007; -.
DR PRIDE; P03007; -.
DR EnsemblBacteria; AAC73320; AAC73320; b0215.
DR EnsemblBacteria; BAA77886; BAA77886; BAA77886.
DR GeneID; 946441; -.
DR KEGG; ecj:JW0205; -.
DR KEGG; eco:b0215; -.
DR PATRIC; fig|511145.12.peg.217; -.
DR EchoBASE; EB0239; -.
DR eggNOG; COG0847; Bacteria.
DR HOGENOM; CLU_047806_2_0_6; -.
DR InParanoid; P03007; -.
DR OMA; FHVYLNP; -.
DR PhylomeDB; P03007; -.
DR BioCyc; EcoCyc:EG10243-MON; -.
DR BioCyc; MetaCyc:EG10243-MON; -.
DR EvolutionaryTrace; P03007; -.
DR PRO; PR:P03007; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009360; C:DNA polymerase III complex; IC:ComplexPortal.
DR GO; GO:0044776; C:DNA polymerase III, core complex; IDA:EcoCyc.
DR GO; GO:0030894; C:replisome; IC:ComplexPortal.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0045004; P:DNA replication proofreading; IMP:EcoCyc.
DR GO; GO:0006261; P:DNA-templated DNA replication; IC:ComplexPortal.
DR GO; GO:0006273; P:lagging strand elongation; IDA:ComplexPortal.
DR GO; GO:0006272; P:leading strand elongation; IDA:ComplexPortal.
DR CDD; cd06131; DNA_pol_III_epsilon_Ecoli_like; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR006054; DnaQ.
DR InterPro; IPR006309; DnaQ_proteo.
DR InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00929; RNase_T; 1.
DR SMART; SM00479; EXOIII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR TIGRFAMs; TIGR00573; dnaq; 1.
DR TIGRFAMs; TIGR01406; dnaQ_proteo; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-directed DNA polymerase; Exonuclease;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..243
FT /note="DNA polymerase III subunit epsilon"
FT /id="PRO_0000105483"
FT ACT_SITE 162
FT /note="Proton acceptor"
FT BINDING 12
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT BINDING 12
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 12
FT /ligand="substrate"
FT BINDING 14
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT BINDING 14
FT /ligand="substrate"
FT BINDING 61
FT /ligand="substrate"
FT BINDING 66
FT /ligand="substrate"
FT BINDING 167
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT BINDING 167
FT /ligand="substrate"
FT MUTAGEN 183..187
FT /note="TSMAF->LSLPL: Increases binding to beta sliding
FT clamp (dnaN), increases stability of enzyme complex."
FT /evidence="ECO:0000269|PubMed:26499492"
FT STRAND 7..16
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 20..23
FT /evidence="ECO:0007829|PDB:2GUI"
FT TURN 24..27
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 30..39
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 60..66
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 70..73
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 79..90
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 93..97
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 100..113
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 130..137
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 145..151
FT /evidence="ECO:0007829|PDB:2GUI"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:2XY8"
FT HELIX 164..178
FT /evidence="ECO:0007829|PDB:2GUI"
FT HELIX 219..236
FT /evidence="ECO:0007829|PDB:4GX8"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:4GX8"
SQ SEQUENCE 243 AA; 27099 MW; 4211C9A00744964F CRC64;
MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVVN RRLTGNNFHV YLKPDRLVDP
EAFGVHGIAD EFLLDKPTFA EVADEFMDYI RGAELVIHNA AFDIGFMDYE FSLLKRDIPK
TNTFCKVTDS LAVARKMFPG KRNSLDALCA RYEIDNSKRT LHGALLDAQI LAEVYLAMTG
GQTSMAFAME GETQQQQGEA TIQRIVRQAS KLRVVFATDE EIAAHEARLD LVQKKGGSCL
WRA
