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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

GO - Biological processi

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.
MetaCyc:EG11414-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11414. holD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001055201 – 137DNA polymerase III subunit psiAdd BLAST137

Proteomic databases

PaxDbiP28632.
PRIDEiP28632.

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
dnaXP06710-22EBI-549176,EBI-2604194
holCP2890522EBI-549176,EBI-549169

Protein-protein interaction databases

BioGridi4262785. 113 interactors.
DIPiDIP-9934N.
IntActiP28632. 22 interactors.
MINTiMINT-1224283.
STRINGi511145.b4372.

Structurei

Secondary structure

1137
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 12Combined sources9
Beta strandi16 – 20Combined sources5
Helixi22 – 24Combined sources3
Beta strandi39 – 42Combined sources4
Helixi52 – 61Combined sources10
Helixi65 – 67Combined sources3
Beta strandi68 – 71Combined sources4
Helixi73 – 76Combined sources4
Beta strandi87 – 91Combined sources5
Beta strandi97 – 100Combined sources4
Beta strandi102 – 105Combined sources4
Helixi108 – 113Combined sources6
Helixi115 – 127Combined sources13
Helixi129 – 132Combined sources4

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP28632.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4108WPU. Bacteria.
COG3050. LUCA.
HOGENOMiHOG000218328.
KOiK02344.
OMAiQICAHEH.

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.
WP_000204012.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77325; AAC77325; b4372.
BAE78360; BAE78360; BAE78360.
GeneIDi948890.
KEGGiecj:JW4334.
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.
WP_000204012.1. NZ_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4262785. 113 interactors.
DIPiDIP-9934N.
IntActiP28632. 22 interactors.
MINTiMINT-1224283.
STRINGi511145.b4372.

Proteomic databases

PaxDbiP28632.
PRIDEiP28632.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77325; AAC77325; b4372.
BAE78360; BAE78360; BAE78360.
GeneIDi948890.
KEGGiecj:JW4334.
eco:b4372.
PATRICi32124354. VBIEscCol129921_4517.

Organism-specific databases

EchoBASEiEB1386.
EcoGeneiEG11414. holD.

Phylogenomic databases

eggNOGiENOG4108WPU. Bacteria.
COG3050. LUCA.
HOGENOMiHOG000218328.
KOiK02344.
OMAiQICAHEH.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP28632.
PROiP28632.

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...

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: November 2, 2016
This is version 134 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

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 one 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.