HOLB_ECOLI
ID HOLB_ECOLI Reviewed; 334 AA.
AC P28631;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=DNA polymerase III subunit delta';
DE EC=2.7.7.7;
GN Name=holB; OrderedLocusNames=b1099, JW1085;
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].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8509334; DOI=10.1128/jb.175.12.3812-3822.1993;
RA Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.;
RT "Identification, isolation, and characterization of the structural gene
RT encoding the delta' subunit of Escherichia coli DNA polymerase III
RT holoenzyme.";
RL J. Bacteriol. 175:3812-3822(1993).
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;
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 [5]
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 [6]
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 [7]
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 [8]
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 [9]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=9363942; DOI=10.1016/s0092-8674(00)80417-1;
RA Guenther B., Onrust R., Sali A., O'Donnell M., Kuriyan J.;
RT "Crystal structure of the delta' subunit of the clamp-loader complex of E.
RT coli DNA polymerase III.";
RL Cell 91:335-345(1997).
RN [10]
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 [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] {ECO:0007744|PDB:1JR3}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH HOLA 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' to 5'
CC exonuclease activity. The gamma complex (gamma(3),delta,delta') is
CC thought to load beta dimers onto DNA by binding ATP which alters the
CC complex's conformation so it can bind beta sliding clamp dimers and
CC open them at one interface. Primed DNA is recognized, ATP is hydrolyzed
CC releasing the gamma complex and closing the beta sliding clamp ring
CC around the primed DNA (PubMed:9927437). {ECO:0000269|PubMed:2040637,
CC ECO:0000269|PubMed:9927437}.
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 P28631; P06710: dnaX; NbExp=26; IntAct=EBI-549161, EBI-549140;
CC P28631; P06710-1: dnaX; NbExp=6; IntAct=EBI-549161, EBI-6464728;
CC P28631; P28630: holA; NbExp=19; IntAct=EBI-549161, EBI-549153;
CC P28631; P28905: holC; NbExp=6; IntAct=EBI-549161, EBI-549169;
CC P28631; P23367: mutL; NbExp=2; IntAct=EBI-549161, EBI-554913;
CC P28631; P0A7M2: rpmB; NbExp=3; IntAct=EBI-549161, EBI-543024;
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DR EMBL; L04577; AAA23708.1; -; Genomic_DNA.
DR EMBL; L01483; AAA23696.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74183.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35906.1; -; Genomic_DNA.
DR PIR; S35523; S35523.
DR RefSeq; NP_415617.1; NC_000913.3.
DR RefSeq; WP_001267956.1; NZ_SSZK01000019.1.
DR PDB; 1A5T; X-ray; 2.20 A; A=1-334.
DR PDB; 1JR3; X-ray; 2.70 A; E=1-334.
DR PDB; 1XXH; X-ray; 3.45 A; E/J=1-334.
DR PDB; 1XXI; X-ray; 4.10 A; E/J=1-334.
DR PDB; 3GLF; X-ray; 3.39 A; E/J=1-334.
DR PDB; 3GLG; X-ray; 3.25 A; E/J=1-334.
DR PDB; 3GLH; X-ray; 3.89 A; E/J/O=1-334.
DR PDB; 3GLI; X-ray; 3.50 A; E/J=1-334.
DR PDBsum; 1A5T; -.
DR PDBsum; 1JR3; -.
DR PDBsum; 1XXH; -.
DR PDBsum; 1XXI; -.
DR PDBsum; 3GLF; -.
DR PDBsum; 3GLG; -.
DR PDBsum; 3GLH; -.
DR PDBsum; 3GLI; -.
DR AlphaFoldDB; P28631; -.
DR SMR; P28631; -.
DR BioGRID; 4263116; 181.
DR BioGRID; 850033; 3.
DR ComplexPortal; CPX-1926; DNA polymerase III clamp loader complex.
DR DIP; DIP-9932N; -.
DR IntAct; P28631; 25.
DR STRING; 511145.b1099; -.
DR jPOST; P28631; -.
DR PaxDb; P28631; -.
DR PRIDE; P28631; -.
DR EnsemblBacteria; AAC74183; AAC74183; b1099.
DR EnsemblBacteria; BAA35906; BAA35906; BAA35906.
DR GeneID; 945661; -.
DR KEGG; ecj:JW1085; -.
DR KEGG; eco:b1099; -.
DR PATRIC; fig|1411691.4.peg.1169; -.
DR EchoBASE; EB1463; -.
DR eggNOG; COG0470; Bacteria.
DR HOGENOM; CLU_006229_4_3_6; -.
DR InParanoid; P28631; -.
DR OMA; YSRCQVW; -.
DR PhylomeDB; P28631; -.
DR BioCyc; EcoCyc:EG11500-MON; -.
DR BioCyc; MetaCyc:EG11500-MON; -.
DR BRENDA; 3.6.4.B8; 2026.
DR EvolutionaryTrace; P28631; -.
DR PRO; PR:P28631; -.
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:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
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; IPR004622; DNA_pol_HolB.
DR InterPro; IPR015199; DNA_pol_III_delta_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF09115; DNApol3-delta_C; 1.
DR SUPFAM; SSF48019; SSF48019; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00678; holB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-directed DNA polymerase;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..334
FT /note="DNA polymerase III subunit delta'"
FT /id="PRO_0000105513"
FT CONFLICT 166
FT /note="P -> G (in Ref. 1; AAA23708)"
FT /evidence="ECO:0000305"
FT HELIX 5..7
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 8..19
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 25..30
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 37..48
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:1XXH"
FT HELIX 63..70
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 90..99
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 139..146
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 153..156
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 184..193
FT /evidence="ECO:0007829|PDB:1A5T"
FT TURN 194..196
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 198..203
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 208..226
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 233..236
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 241..255
FT /evidence="ECO:0007829|PDB:1A5T"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:3GLG"
FT HELIX 271..280
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 283..303
FT /evidence="ECO:0007829|PDB:1A5T"
FT HELIX 308..322
FT /evidence="ECO:0007829|PDB:1A5T"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:1XXH"
SQ SEQUENCE 334 AA; 36937 MW; DC9DAA644AD8A096 CRC64;
MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG
HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL NEHARLGGAK VVWVTDAALL
TDAAANALLK TLEEPPAETW FFLATREPER LLATLRSRCR LHYLAPPPEQ YAVTWLSREV
TMSQDALLAA LRLSAGSPGA ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ
APARLHWLAT LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL
MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL
