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Protein

DNA polymerase III subunit delta

Gene

holA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 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 delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA.

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

  • DNA-dependent DNA replication Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Enzyme and pathway databases

BioCyciEcoCyc:EG11412-MONOMER.
ECOL316407:JW0635-MONOMER.
MetaCyc:EG11412-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase III subunit delta (EC:2.7.7.7)
Gene namesi
Name:holA
Ordered Locus Names:b0640, JW0635
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11412. holA.

Subcellular locationi

GO - Cellular componenti

  • DNA polymerase III complex Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001055051 – 343DNA polymerase III subunit deltaAdd BLAST343

Proteomic databases

PaxDbiP28630.
PRIDEiP28630.

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
dnaEP104434EBI-549153,EBI-549111
dnaNP0A98810EBI-549153,EBI-542385
dnaXP06710-15EBI-549153,EBI-6464728
dnaXP06710-26EBI-549153,EBI-2604194
holBP2863117EBI-549153,EBI-549161
mutLP233672EBI-549153,EBI-554913
nfsAP171173EBI-549153,EBI-1120624
yeeWP645262EBI-549153,EBI-9146863

Protein-protein interaction databases

BioGridi4259908. 201 interactors.
DIPiDIP-9931N.
IntActiP28630. 49 interactors.
MINTiMINT-1235044.
STRINGi511145.b0640.

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Helixi6 – 8Combined sources3
Helixi9 – 15Combined sources7
Beta strandi19 – 26Combined sources8
Helixi28 – 44Combined sources17
Beta strandi49 – 51Combined sources3
Helixi61 – 69Combined sources9
Beta strandi73 – 76Combined sources4
Beta strandi78 – 83Combined sources6
Helixi93 – 103Combined sources11
Beta strandi106 – 108Combined sources3
Beta strandi110 – 113Combined sources4
Helixi121 – 123Combined sources3
Helixi125 – 130Combined sources6
Helixi131 – 133Combined sources3
Beta strandi135 – 138Combined sources4
Turni144 – 146Combined sources3
Helixi147 – 156Combined sources10
Turni157 – 159Combined sources3
Helixi164 – 174Combined sources11
Helixi178 – 191Combined sources14
Helixi199 – 206Combined sources8
Helixi214 – 222Combined sources9
Helixi226 – 235Combined sources10
Turni236 – 240Combined sources5
Turni243 – 245Combined sources3
Helixi246 – 261Combined sources16
Turni262 – 266Combined sources5
Turni269 – 275Combined sources7
Helixi280 – 282Combined sources3
Turni283 – 285Combined sources3
Helixi286 – 292Combined sources7
Helixi295 – 314Combined sources20
Helixi325 – 331Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90C/D1-343[»]
1JQLX-ray2.50B1-140[»]
1JR3X-ray2.70D1-343[»]
1XXHX-ray3.45A/F1-343[»]
1XXIX-ray4.10A/F1-343[»]
3GLFX-ray3.39A/F1-343[»]
3GLGX-ray3.25A/F1-343[»]
3GLHX-ray3.89A/F/K1-343[»]
3GLIX-ray3.50A/F1-343[»]
ProteinModelPortaliP28630.
SMRiP28630.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28630.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4105DJF. Bacteria.
COG1466. LUCA.
HOGENOMiHOG000256204.
InParanoidiP28630.
KOiK02340.
OMAiRQQGFDE.
PhylomeDBiP28630.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR032780. DNA_pol3_delt_C.
IPR010372. DNA_pol3_delta_N.
IPR005790. DNA_polIII_delta.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF14840. DNA_pol3_delt_C. 1 hit.
PF06144. DNA_pol3_delta. 1 hit.
[Graphical view]
SUPFAMiSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01128. holA. 1 hit.

Sequencei

Sequence statusi: Complete.

P28630-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH
60 70 80 90 100
HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL
110 120 130 140 150
TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW
160 170 180 190 200
VAARAKQLNL ELDDAANQVL CYCYEGNLLA LAQALERLSL LWPDGKLTLP
210 220 230 240 250
RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG SEPVILLRTL
260 270 280 290 300
QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ
310 320 330 340
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG
Length:343
Mass (Da):38,704
Last modified:December 1, 1992 - v1
Checksum:i87239A678FE16BE2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04576 Genomic DNA. Translation: AAA23675.1.
M94267 Genomic DNA. Translation: AAB59047.1.
U82598 Genomic DNA. Translation: AAB40841.1.
U00096 Genomic DNA. Translation: AAC73741.1.
AP009048 Genomic DNA. Translation: BAA35287.1.
M18277 Genomic DNA. No translation available.
PIRiA45251.
RefSeqiNP_415173.1. NC_000913.3.
WP_000620535.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640.
BAA35287; BAA35287; BAA35287.
GeneIDi947573.
KEGGiecj:JW0635.
eco:b0640.
PATRICi32116463. VBIEscCol129921_0671.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04576 Genomic DNA. Translation: AAA23675.1.
M94267 Genomic DNA. Translation: AAB59047.1.
U82598 Genomic DNA. Translation: AAB40841.1.
U00096 Genomic DNA. Translation: AAC73741.1.
AP009048 Genomic DNA. Translation: BAA35287.1.
M18277 Genomic DNA. No translation available.
PIRiA45251.
RefSeqiNP_415173.1. NC_000913.3.
WP_000620535.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90C/D1-343[»]
1JQLX-ray2.50B1-140[»]
1JR3X-ray2.70D1-343[»]
1XXHX-ray3.45A/F1-343[»]
1XXIX-ray4.10A/F1-343[»]
3GLFX-ray3.39A/F1-343[»]
3GLGX-ray3.25A/F1-343[»]
3GLHX-ray3.89A/F/K1-343[»]
3GLIX-ray3.50A/F1-343[»]
ProteinModelPortaliP28630.
SMRiP28630.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259908. 201 interactors.
DIPiDIP-9931N.
IntActiP28630. 49 interactors.
MINTiMINT-1235044.
STRINGi511145.b0640.

Proteomic databases

PaxDbiP28630.
PRIDEiP28630.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640.
BAA35287; BAA35287; BAA35287.
GeneIDi947573.
KEGGiecj:JW0635.
eco:b0640.
PATRICi32116463. VBIEscCol129921_0671.

Organism-specific databases

EchoBASEiEB1384.
EcoGeneiEG11412. holA.

Phylogenomic databases

eggNOGiENOG4105DJF. Bacteria.
COG1466. LUCA.
HOGENOMiHOG000256204.
InParanoidiP28630.
KOiK02340.
OMAiRQQGFDE.
PhylomeDBiP28630.

Enzyme and pathway databases

BioCyciEcoCyc:EG11412-MONOMER.
ECOL316407:JW0635-MONOMER.
MetaCyc:EG11412-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP28630.
PROiP28630.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR032780. DNA_pol3_delt_C.
IPR010372. DNA_pol3_delta_N.
IPR005790. DNA_polIII_delta.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF14840. DNA_pol3_delt_C. 1 hit.
PF06144. DNA_pol3_delta. 1 hit.
[Graphical view]
SUPFAMiSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01128. holA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHOLA_ECOLI
AccessioniPrimary (citable) accession number: P28630
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: November 2, 2016
This is version 144 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, Direct protein sequencing, 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.