HOLA_ECOLI
ID HOLA_ECOLI Reviewed; 343 AA.
AC P28630;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-1992, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=DNA polymerase III subunit delta;
DE EC=2.7.7.7;
GN Name=holA; OrderedLocusNames=b0640, JW0635;
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=8505303; DOI=10.1016/s0021-9258(19)50264-2;
RA Dong Z., Onrust R., Skangalis M., O'Donnell M.;
RT "DNA polymerase III accessory proteins. I. holA and holB encoding delta and
RT delta'.";
RL J. Biol. Chem. 268:11758-11765(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1400251; DOI=10.1128/jb.174.21.7013-7025.1992;
RA Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.;
RT "Molecular cloning, sequencing, and overexpression of the structural gene
RT encoding the delta subunit of Escherichia coli DNA polymerase III
RT holoenzyme.";
RL J. Bacteriol. 174:7013-7025(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [4]
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 [5]
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 [6]
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 [7]
RP PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
RC STRAIN=K12;
RX PubMed=3316191; DOI=10.1128/jb.169.12.5692-5699.1987;
RA Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H.,
RA Ohta T., Matsuhashi M.;
RT "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia
RT coli chromosome.";
RL J. Bacteriol. 169:5692-5699(1987).
RN [8]
RP FUNCTION, AND SUBUNIT.
RX PubMed=2040637; DOI=10.1016/s0021-9258(18)99166-0;
RA Stukenberg P.T., Studwell-Vaughan P.S., O'Donnell M.;
RT "Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme.";
RL J. Biol. Chem. 266:11328-11334(1991).
RN [9]
RP CHARACTERIZATION.
RX PubMed=8505304; DOI=10.1016/s0021-9258(19)50265-4;
RA Onrust R., O'Donnell M.;
RT "DNA polymerase III accessory proteins. II. Characterization of delta and
RT delta'.";
RL J. Biol. Chem. 268:11766-11772(1993).
RN [10]
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 [11]
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 [12]
RP FUNCTION, AND SUBUNIT.
RX PubMed=9927437; DOI=10.1093/emboj/18.3.771;
RA Turner J., Hingorani M.M., Kelman Z., O'Donnell M.;
RT "The internal workings of a DNA polymerase clamp-loading machine.";
RL EMBO J. 18:771-783(1999).
RN [13]
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 [14]
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 [15] {ECO:0007744|PDB:1JQJ, ECO:0007744|PDB:1JQL}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH BETA SLIDING-CLAMP
RP (DNAN), FUNCTION, AND DOMAIN.
RX PubMed=11525728; DOI=10.1016/s0092-8674(01)00462-7;
RA Jeruzalmi D., Yurieva O., Zhao Y., Young M., Stewart J., Hingorani M.,
RA O'Donnell M., Kuriyan J.;
RT "Mechanism of processivity clamp opening by the delta subunit wrench of the
RT clamp loader complex of E. coli DNA polymerase III.";
RL Cell 106:417-428(2001).
RN [16] {ECO:0007744|PDB:1JR3}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH HOLB AND DNAX
RP (ISOFORM GAMMA).
RX PubMed=11525729; DOI=10.1016/s0092-8674(01)00463-9;
RA Jeruzalmi D., O'Donnell M., Kuriyan J.;
RT "Crystal structure of the processivity clamp loader gamma (gamma) complex
RT of E. coli DNA polymerase III.";
RL Cell 106:429-441(2001).
CC -!- FUNCTION: Part of the beta sliding clamp loading complex, which
CC hydrolyzes ATP to load the beta clamp onto primed DNA to form the DNA
CC replication pre-initiation complex (PubMed:2040637). DNA polymerase III
CC is a complex, multichain enzyme responsible for most of the replicative
CC synthesis in bacteria. This DNA polymerase also exhibits 3'-5'
CC exonuclease activity. The delta subunit is the wrench that will open
CC the beta subunit dimer, which has been modeled to leave a gap large
CC enough for ssDNA to pass through (PubMed:11525728). The gamma complex
CC (gamma(3),delta,delta') is thought to load beta dimers onto DNA by
CC binding ATP which alters the complex's conformation so it can bind beta
CC sliding clamp dimers and open them at one interface. Primed DNA is
CC recognized, ATP is hydrolyzed releasing the gamma complex and closing
CC the beta sliding clamp ring around the primed DNA (PubMed:9927437).
CC {ECO:0000269|PubMed:2040637, ECO:0000269|PubMed:9927437,
CC ECO:0000305|PubMed:11525728}.
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: The DNA polymerase III holoenzyme complex contains at least 10
CC 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:2040637). The polymerase is tethered to
CC the template via the dimeric beta sliding clamp processivity factor.
CC The clamp-loading complex (also called gamma complex) assembles the
CC beta sliding clamp onto the primed template and plays a central role in
CC the 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). The clamp loader hydrolyzes ATP to
CC assemble the beta processivity factor onto the primed template
CC (PubMed:2040637, PubMed:9927437) and plays a central role in the
CC organization and communication at the replication fork; the minimal
CC complex to load the beta sliding clamp on DNA is delta, delta', gamma
CC (PubMed:9927437). {ECO:0000269|PubMed:11525729,
CC ECO:0000269|PubMed:2040637, ECO:0000269|PubMed:20413500,
CC ECO:0000269|PubMed:22157955, ECO:0000269|PubMed:9927437}.
CC -!- INTERACTION:
CC P28630; P10443: dnaE; NbExp=5; IntAct=EBI-549153, EBI-549111;
CC P28630; P0A988: dnaN; NbExp=10; IntAct=EBI-549153, EBI-542385;
CC P28630; P03007: dnaQ; NbExp=3; IntAct=EBI-549153, EBI-549131;
CC P28630; P06710: dnaX; NbExp=19; IntAct=EBI-549153, EBI-549140;
CC P28630; P06710-1: dnaX; NbExp=5; IntAct=EBI-549153, EBI-6464728;
CC P28630; P06710-2: dnaX; NbExp=6; IntAct=EBI-549153, EBI-2604194;
CC P28630; P28631: holB; NbExp=19; IntAct=EBI-549153, EBI-549161;
CC P28630; P23367: mutL; NbExp=2; IntAct=EBI-549153, EBI-554913;
CC P28630; P17117: nfsA; NbExp=3; IntAct=EBI-549153, EBI-1120624;
CC P28630; P64526: yeeW; NbExp=2; IntAct=EBI-549153, EBI-9146863;
CC -!- DOMAIN: Has three domains, each of which is closely related to a
CC corresponding domain in the delta' stator, despite the 2 proteins
CC having only 6-8% sequence identity. Interacts with the beta sliding
CC clamp via domain 1 (residues 1-140, in particular residues 61-74),
CC fitting into a cleft between domains 2 and 3 on the surface of the
CC beta-clamp (PubMed:11525728). Residues 61-74 move about 45 degrees and
CC 5.5 Angstroms in the beta-delta versus gamma-delta-delta' structure to
CC contact respectively the beta or delta' (PubMed:11525728).
CC {ECO:0000269|PubMed:11525728}.
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; L04576; AAA23675.1; -; Genomic_DNA.
DR EMBL; M94267; AAB59047.1; -; Genomic_DNA.
DR EMBL; U82598; AAB40841.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73741.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35287.1; -; Genomic_DNA.
DR EMBL; M18277; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A45251; A45251.
DR RefSeq; NP_415173.1; NC_000913.3.
DR RefSeq; WP_000620535.1; NZ_SSZK01000037.1.
DR PDB; 1JQJ; X-ray; 2.90 A; C/D=1-343.
DR PDB; 1JQL; X-ray; 2.50 A; B=1-140.
DR PDB; 1JR3; X-ray; 2.70 A; D=1-343.
DR PDB; 1XXH; X-ray; 3.45 A; A/F=1-343.
DR PDB; 1XXI; X-ray; 4.10 A; A/F=1-343.
DR PDB; 3GLF; X-ray; 3.39 A; A/F=1-343.
DR PDB; 3GLG; X-ray; 3.25 A; A/F=1-343.
DR PDB; 3GLH; X-ray; 3.89 A; A/F/K=1-343.
DR PDB; 3GLI; X-ray; 3.50 A; A/F=1-343.
DR PDBsum; 1JQJ; -.
DR PDBsum; 1JQL; -.
DR PDBsum; 1JR3; -.
DR PDBsum; 1XXH; -.
DR PDBsum; 1XXI; -.
DR PDBsum; 3GLF; -.
DR PDBsum; 3GLG; -.
DR PDBsum; 3GLH; -.
DR PDBsum; 3GLI; -.
DR AlphaFoldDB; P28630; -.
DR SMR; P28630; -.
DR BioGRID; 4259908; 201.
DR BioGRID; 851889; 23.
DR ComplexPortal; CPX-1926; DNA polymerase III clamp loader complex.
DR DIP; DIP-9931N; -.
DR IntAct; P28630; 49.
DR STRING; 511145.b0640; -.
DR jPOST; P28630; -.
DR PaxDb; P28630; -.
DR PRIDE; P28630; -.
DR EnsemblBacteria; AAC73741; AAC73741; b0640.
DR EnsemblBacteria; BAA35287; BAA35287; BAA35287.
DR GeneID; 947573; -.
DR KEGG; ecj:JW0635; -.
DR KEGG; eco:b0640; -.
DR PATRIC; fig|1411691.4.peg.1628; -.
DR EchoBASE; EB1384; -.
DR eggNOG; COG1466; Bacteria.
DR HOGENOM; CLU_044694_0_2_6; -.
DR InParanoid; P28630; -.
DR OMA; RIPTGKP; -.
DR PhylomeDB; P28630; -.
DR BioCyc; EcoCyc:EG11412-MON; -.
DR BioCyc; MetaCyc:EG11412-MON; -.
DR BRENDA; 3.6.4.B8; 2026.
DR EvolutionaryTrace; P28630; -.
DR PRO; PR:P28630; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009360; C:DNA polymerase III complex; IDA:EcoCyc.
DR GO; GO:0043846; C:DNA polymerase III, clamp loader complex; IPI:ComplexPortal.
DR GO; GO:0030894; C:replisome; IC:ComplexPortal.
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:0006260; P:DNA replication; IC:ComplexPortal.
DR GO; GO:0006261; P:DNA-templated DNA replication; IDA:EcoCyc.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR008921; DNA_pol3_clamp-load_cplx_C.
DR InterPro; IPR032780; DNA_pol3_delt_C.
DR InterPro; IPR010372; DNA_pol3_delta_N.
DR InterPro; IPR005790; DNA_polIII_delta.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF14840; DNA_pol3_delt_C; 1.
DR Pfam; PF06144; DNA_pol3_delta; 1.
DR SUPFAM; SSF48019; SSF48019; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01128; holA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA replication;
KW DNA-directed DNA polymerase; Nucleotidyltransferase; Reference proteome;
KW Transferase.
FT CHAIN 1..343
FT /note="DNA polymerase III subunit delta"
FT /id="PRO_0000105505"
FT REGION 1..140
FT /note="Domain 1"
FT /evidence="ECO:0000305|PubMed:11525728"
FT REGION 141..210
FT /note="Domain 2"
FT /evidence="ECO:0000305|PubMed:11525728"
FT REGION 211..343
FT /note="Domain 3"
FT /evidence="ECO:0000305|PubMed:11525728"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 9..15
FT /evidence="ECO:0007829|PDB:1JQL"
FT STRAND 19..26
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 28..44
FT /evidence="ECO:0007829|PDB:1JQL"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 61..69
FT /evidence="ECO:0007829|PDB:1JQL"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:3GLG"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 93..103
FT /evidence="ECO:0007829|PDB:1JQL"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:3GLG"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 125..130
FT /evidence="ECO:0007829|PDB:1JQL"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:1JQL"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:1JQL"
FT TURN 144..146
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 147..156
FT /evidence="ECO:0007829|PDB:1JQJ"
FT TURN 157..159
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 164..174
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 178..191
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 199..206
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 226..235
FT /evidence="ECO:0007829|PDB:1JQJ"
FT TURN 236..240
FT /evidence="ECO:0007829|PDB:1JQJ"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 246..261
FT /evidence="ECO:0007829|PDB:1JQJ"
FT TURN 262..266
FT /evidence="ECO:0007829|PDB:1JQJ"
FT TURN 269..275
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 280..282
FT /evidence="ECO:0007829|PDB:3GLG"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 286..292
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 295..314
FT /evidence="ECO:0007829|PDB:1JQJ"
FT HELIX 325..331
FT /evidence="ECO:0007829|PDB:1JQJ"
SQ SEQUENCE 343 AA; 38704 MW; 87239A678FE16BE2 CRC64;
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD
WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA
QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL CYCYEGNLLA
LAQALERLSL LWPDGKLTLP RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG
SEPVILLRTL QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG
