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P28630 (HOLA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase III subunit delta

EC=2.7.7.7
Gene names
Name:holA
Ordered Locus Names:b0640, JW0635
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length343 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Subunit structure

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].

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 343343DNA polymerase III subunit delta
PRO_0000105505

Secondary structure

............................................................ 343
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P28630 [UniParc].

Last modified December 1, 1992. Version 1.
Checksum: 87239A678FE16BE2

FASTA34338,704
        10         20         30         40         50         60 
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD 

        70         80         90        100        110        120 
WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA 

       130        140        150        160        170        180 
QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL CYCYEGNLLA 

       190        200        210        220        230        240 
LAQALERLSL LWPDGKLTLP RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG 

       250        260        270        280        290        300 
SEPVILLRTL QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ 

       310        320        330        340 
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG 

« Hide

References

« Hide 'large scale' references
[1]"DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'."
Dong Z., Onrust R., Skangalis M., O'Donnell M.
J. Biol. Chem. 268:11758-11765(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"Molecular cloning, sequencing, and overexpression of the structural gene encoding the delta subunit of Escherichia coli DNA polymerase III holoenzyme."
Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
J. Bacteriol. 174:7013-7025(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
Strain: K12 / MG1655 / ATCC 47076.
[3]"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map."
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. expand/collapse author list , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T.
DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Sequence of minutes 4-25 of Escherichia coli."
Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome."
Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H., Ohta T., Matsuhashi M.
J. Bacteriol. 169:5692-5699(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
Strain: K12.
[8]"DNA polymerase III accessory proteins. II. Characterization of delta and delta'."
Onrust R., O'Donnell M.
J. Biol. Chem. 268:11766-11772(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[9]"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.
[10]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA45251.
RefSeqNP_415173.1. NC_000913.3.
YP_488931.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP28630.
SMRP28630. Positions 1-338.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9931N.
IntActP28630. 49 interactions.
MINTMINT-1235044.
STRING511145.b0640.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73741; AAC73741; b0640.
BAA35287; BAA35287; BAA35287.
GeneID12930914.
947573.
KEGGecj:Y75_p0630.
eco:b0640.
PATRIC32116463. VBIEscCol129921_0671.

Organism-specific databases

EchoBASEEB1384.
EcoGeneEG11412. holA.

Phylogenomic databases

eggNOGCOG1466.
HOGENOMHOG000256204.
KOK02340.
OMAADRVEGN.
OrthoDBEOG6BCSPJ.
ProtClustDBPRK05574.

Enzyme and pathway databases

BioCycEcoCyc:EG11412-MONOMER.
ECOL316407:JW0635-MONOMER.

Gene expression databases

GenevestigatorP28630.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR010372. DNA_pol3_delta.
IPR005790. DNA_polIII_delta.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF06144. DNA_pol3_delta. 1 hit.
[Graphical view]
SUPFAMSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR01128. holA. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP28630.
PROP28630.

Entry information

Entry nameHOLA_ECOLI
AccessionPrimary (citable) accession number: P28630
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: April 16, 2014
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene