HOLD_ECOLI
ID HOLD_ECOLI Reviewed; 137 AA.
AC P28632; Q2M5U6;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-1992, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=DNA polymerase III subunit psi;
DE EC=2.7.7.7;
GN Name=holD; OrderedLocusNames=b4372, JW4334;
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=8389364; DOI=10.1016/s0021-9258(19)50266-6;
RA Xiao H., Crombie R., Dong Z., Onrust R., O'Donnell M.;
RT "DNA polymerase III accessory proteins. III. holC and holD encoding chi and
RT psi.";
RL J. Biol. Chem. 268:11773-11778(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8366044; DOI=10.1128/jb.175.17.5604-5610.1993;
RA Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.;
RT "Identification, isolation, and overexpression of the gene encoding the psi
RT subunit of DNA polymerase III holoenzyme.";
RL J. Bacteriol. 175:5604-5610(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2828880; DOI=10.1007/bf00331153;
RA Yoshikawa A., Isono S., Sheback A., Isono K.;
RT "Cloning and nucleotide sequencing of the genes rimI and rimJ which encode
RT enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli
RT K12.";
RL Mol. Gen. Genet. 209:481-488(1987).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
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 CHARACTERIZATION.
RX PubMed=8505305; DOI=10.1016/s0021-9258(19)50267-8;
RA Xiao H., Dong Z., O'Donnell M.;
RT "DNA polymerase III accessory proteins. IV. Characterization of chi and
RT psi.";
RL J. Biol. Chem. 268:11779-11784(1993).
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 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 [10]
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 [11]
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 [12]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-137.
RX PubMed=14717711; DOI=10.1046/j.1432-1033.2003.03944.x;
RA Gulbis J.M., Kazmirski S.L., Finkelstein J., Kelman Z., O'Donnell M.,
RA Kuriyan J.;
RT "Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA
RT polymerase clamp-loader complex.";
RL Eur. J. Biochem. 271:439-449(2004).
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 exact function of the psi subunit is unknown.
CC {ECO:0000269|PubMed:2040637}.
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) and plays a central role in the organization and
CC communication at the replication fork. {ECO:0000269|PubMed:2040637,
CC ECO:0000269|PubMed:20413500, ECO:0000269|PubMed:22157955}.
CC -!- INTERACTION:
CC P28632; P06710: dnaX; NbExp=26; IntAct=EBI-549176, EBI-549140;
CC P28632; P06710-2: dnaX; NbExp=2; IntAct=EBI-549176, EBI-2604194;
CC P28632; P28905: holC; NbExp=25; IntAct=EBI-549176, EBI-549169;
CC P28632; P14294: topB; NbExp=3; IntAct=EBI-549176, EBI-552080;
CC P28632; P76092: ynbC; NbExp=3; IntAct=EBI-549176, EBI-544837;
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DR EMBL; L04575; AAA24435.1; -; Genomic_DNA.
DR EMBL; L05387; AAA03076.1; -; Unassigned_DNA.
DR EMBL; X06117; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U14003; AAA97268.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77325.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78360.1; -; Genomic_DNA.
DR PIR; A48647; A48647.
DR RefSeq; NP_418789.1; NC_000913.3.
DR RefSeq; WP_000204012.1; NZ_LN832404.1.
DR PDB; 1EM8; X-ray; 2.10 A; B/D=26-137.
DR PDB; 3GLI; X-ray; 3.50 A; O/P=2-28.
DR PDB; 3SXU; X-ray; 1.85 A; B=2-137.
DR PDBsum; 1EM8; -.
DR PDBsum; 3GLI; -.
DR PDBsum; 3SXU; -.
DR AlphaFoldDB; P28632; -.
DR SMR; P28632; -.
DR BioGRID; 4262785; 117.
DR BioGRID; 853167; 4.
DR ComplexPortal; CPX-1926; DNA polymerase III clamp loader complex.
DR DIP; DIP-9934N; -.
DR IntAct; P28632; 23.
DR MINT; P28632; -.
DR STRING; 511145.b4372; -.
DR jPOST; P28632; -.
DR PaxDb; P28632; -.
DR PRIDE; P28632; -.
DR EnsemblBacteria; AAC77325; AAC77325; b4372.
DR EnsemblBacteria; BAE78360; BAE78360; BAE78360.
DR GeneID; 948890; -.
DR KEGG; ecj:JW4334; -.
DR KEGG; eco:b4372; -.
DR PATRIC; fig|1411691.4.peg.2316; -.
DR EchoBASE; EB1386; -.
DR eggNOG; COG3050; Bacteria.
DR HOGENOM; CLU_132082_0_0_6; -.
DR OMA; QICAHEH; -.
DR PhylomeDB; P28632; -.
DR BioCyc; EcoCyc:EG11414-MON; -.
DR BioCyc; MetaCyc:EG11414-MON; -.
DR BRENDA; 3.6.4.B8; 2026.
DR EvolutionaryTrace; P28632; -.
DR PRO; PR:P28632; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009360; C:DNA polymerase III complex; IC:ComplexPortal.
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: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; IC:ComplexPortal.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR Gene3D; 3.40.50.10220; -; 1.
DR InterPro; IPR004615; DNA_pol_III_psi.
DR InterPro; IPR036654; DNA_pol_III_psi_sf.
DR InterPro; IPR018382; DNA_pol_III_psi_subgr.
DR Pfam; PF03603; DNA_III_psi; 1.
DR PIRSF; PIRSF029225; DNA_pol_III_psi; 1.
DR SUPFAM; SSF102220; SSF102220; 1.
DR TIGRFAMs; TIGR00664; DNA_III_psi; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-directed DNA polymerase;
KW Nucleotidyltransferase; Reference proteome; Transferase.
FT CHAIN 1..137
FT /note="DNA polymerase III subunit psi"
FT /id="PRO_0000105520"
FT HELIX 4..12
FT /evidence="ECO:0007829|PDB:3GLI"
FT STRAND 16..20
FT /evidence="ECO:0007829|PDB:3GLI"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:3GLI"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 52..61
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:3SXU"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 73..76
FT /evidence="ECO:0007829|PDB:3SXU"
FT STRAND 87..91
FT /evidence="ECO:0007829|PDB:3SXU"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:1EM8"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:3SXU"
FT HELIX 129..132
FT /evidence="ECO:0007829|PDB:3SXU"
SQ SEQUENCE 137 AA; 15174 MW; 5B7356201E7E27FE CRC64;
MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT DPLVSDVLRA
LTVSPDQVLQ LTPEKIAMLP QGSHCNSWRL GTDEPLSLEG AQVASPALTD LRANPTARAA
LWQQICTYEH DFFPRND
