Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA polymerase III subunit psi

Gene

holD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The exact function of the psi subunit is unknown.

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: InterPro
  2. DNA-directed DNA polymerase activity Source: UniProtKB-KW

GO - Biological processi

  1. DNA replication Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Enzyme and pathway databases

BioCyciEcoCyc:EG11414-MONOMER.
ECOL316407:JW4334-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase III subunit psi (EC:2.7.7.7)
Gene namesi
Name:holD
Ordered Locus Names:b4372, JW4334
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11414. holD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 137137DNA polymerase III subunit psiPRO_0000105520Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP28632.

Interactioni

Subunit structurei

The DNA polymerase holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential subassemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core (subunits alpha,epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. This complex contains delta, delta', psi and chi, and copies of either or both of two different DnaX proteins, gamma and tau. The composition of the holoenzyme is, therefore: (alpha,epsilon,theta)[2]-(gamma/tau)[3]-delta,delta', psi,chi-beta[4].

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaXP0671018EBI-549176,EBI-549140
holCP2890522EBI-549176,EBI-549169

Protein-protein interaction databases

DIPiDIP-9934N.
IntActiP28632. 22 interactions.
MINTiMINT-1224283.
STRINGi511145.b4372.

Structurei

Secondary structure

1
137
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 129Combined sources
Beta strandi16 – 205Combined sources
Helixi22 – 243Combined sources
Beta strandi39 – 424Combined sources
Helixi52 – 6110Combined sources
Helixi65 – 673Combined sources
Beta strandi68 – 714Combined sources
Helixi73 – 764Combined sources
Beta strandi87 – 915Combined sources
Beta strandi97 – 1004Combined sources
Beta strandi102 – 1054Combined sources
Helixi108 – 1136Combined sources
Helixi115 – 12713Combined sources
Helixi129 – 1324Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EM8X-ray2.10B/D26-137[»]
3GLIX-ray3.50O/P2-28[»]
3SXUX-ray1.85B2-137[»]
ProteinModelPortaliP28632.
SMRiP28632. Positions 2-137.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28632.

Family & Domainsi

Phylogenomic databases

eggNOGiCOG3050.
HOGENOMiHOG000218328.
KOiK02344.
OMAiQICAHEH.
OrthoDBiEOG6WDSJJ.

Family and domain databases

Gene3Di3.40.50.10220. 1 hit.
InterProiIPR004615. DNA_pol_III_psi.
IPR018382. DNA_pol_III_psi_subgr.
[Graphical view]
PfamiPF03603. DNA_III_psi. 1 hit.
[Graphical view]
PIRSFiPIRSF029225. DNA_pol_III_psi. 1 hit.
ProDomiPD032475. DNA_pol_III_psi. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF102220. SSF102220. 1 hit.
TIGRFAMsiTIGR00664. DNA_III_psi. 1 hit.

Sequencei

Sequence statusi: Complete.

P28632-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT
60 70 80 90 100
DPLVSDVLRA LTVSPDQVLQ LTPEKIAMLP QGSHCNSWRL GTDEPLSLEG
110 120 130
AQVASPALTD LRANPTARAA LWQQICTYEH DFFPRND
Length:137
Mass (Da):15,174
Last modified:December 1, 1992 - v1
Checksum:i5B7356201E7E27FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04575 Genomic DNA. Translation: AAA24435.1.
L05387 Unassigned DNA. Translation: AAA03076.1.
X06117 Genomic DNA. No translation available.
U14003 Genomic DNA. Translation: AAA97268.1.
U00096 Genomic DNA. Translation: AAC77325.1.
AP009048 Genomic DNA. Translation: BAE78360.1.
PIRiA48647.
RefSeqiNP_418789.1. NC_000913.3.
YP_492501.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC77325; AAC77325; b4372.
BAE78360; BAE78360; BAE78360.
GeneIDi12933791.
948890.
KEGGiecj:Y75_p4255.
eco:b4372.
PATRICi32124354. VBIEscCol129921_4517.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04575 Genomic DNA. Translation: AAA24435.1.
L05387 Unassigned DNA. Translation: AAA03076.1.
X06117 Genomic DNA. No translation available.
U14003 Genomic DNA. Translation: AAA97268.1.
U00096 Genomic DNA. Translation: AAC77325.1.
AP009048 Genomic DNA. Translation: BAE78360.1.
PIRiA48647.
RefSeqiNP_418789.1. NC_000913.3.
YP_492501.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EM8X-ray2.10B/D26-137[»]
3GLIX-ray3.50O/P2-28[»]
3SXUX-ray1.85B2-137[»]
ProteinModelPortaliP28632.
SMRiP28632. Positions 2-137.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9934N.
IntActiP28632. 22 interactions.
MINTiMINT-1224283.
STRINGi511145.b4372.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77325; AAC77325; b4372.
BAE78360; BAE78360; BAE78360.
GeneIDi12933791.
948890.
KEGGiecj:Y75_p4255.
eco:b4372.
PATRICi32124354. VBIEscCol129921_4517.

Organism-specific databases

EchoBASEiEB1386.
EcoGeneiEG11414. holD.

Phylogenomic databases

eggNOGiCOG3050.
HOGENOMiHOG000218328.
KOiK02344.
OMAiQICAHEH.
OrthoDBiEOG6WDSJJ.

Enzyme and pathway databases

BioCyciEcoCyc:EG11414-MONOMER.
ECOL316407:JW4334-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP28632.
PROiP28632.

Gene expression databases

GenevestigatoriP28632.

Family and domain databases

Gene3Di3.40.50.10220. 1 hit.
InterProiIPR004615. DNA_pol_III_psi.
IPR018382. DNA_pol_III_psi_subgr.
[Graphical view]
PfamiPF03603. DNA_III_psi. 1 hit.
[Graphical view]
PIRSFiPIRSF029225. DNA_pol_III_psi. 1 hit.
ProDomiPD032475. DNA_pol_III_psi. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF102220. SSF102220. 1 hit.
TIGRFAMsiTIGR00664. DNA_III_psi. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi."
    Xiao H., Crombie R., Dong Z., Onrust R., O'Donnell M.
    J. Biol. Chem. 268:11773-11778(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Identification, isolation, and overexpression of the gene encoding the psi subunit of DNA polymerase III holoenzyme."
    Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
    J. Bacteriol. 175:5604-5610(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12."
    Yoshikawa A., Isono S., Sheback A., Isono K.
    Mol. Gen. Genet. 209:481-488(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  4. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. "DNA polymerase III accessory proteins. IV. Characterization of chi and psi."
    Xiao H., Dong Z., O'Donnell M.
    J. Biol. Chem. 268:11779-11784(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  8. "Accessory protein function in the DNA polymerase III holoenzyme from E. coli."
    O'Donnell M.
    Bioessays 14:105-111(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  9. "Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex."
    Gulbis J.M., Kazmirski S.L., Finkelstein J., Kelman Z., O'Donnell M., Kuriyan J.
    Eur. J. Biochem. 271:439-449(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-137.

Entry informationi

Entry nameiHOLD_ECOLI
AccessioniPrimary (citable) accession number: P28632
Secondary accession number(s): Q2M5U6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: January 7, 2015
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.