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P28631 (HOLB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 132. 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:holB
Ordered Locus Names:b1099, JW1085
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length334 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.

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 – 334334DNA polymerase III subunit delta'
PRO_0000105513

Experimental info

Sequence conflict1661P → G in AAA23708. Ref.1

Secondary structure

........................................................ 334
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P28631 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: DC9DAA644AD8A096

FASTA33436,937
        10         20         30         40         50         60 
MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG 

        70         80         90        100        110        120 
HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL NEHARLGGAK VVWVTDAALL 

       130        140        150        160        170        180 
TDAAANALLK TLEEPPAETW FFLATREPER LLATLRSRCR LHYLAPPPEQ YAVTWLSREV 

       190        200        210        220        230        240 
TMSQDALLAA LRLSAGSPGA ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ 

       250        260        270        280        290        300 
APARLHWLAT LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL 

       310        320        330 
MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL 

« 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]"Identification, isolation, and characterization 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. 175:3812-3822(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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]"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.
[5]"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.
[6]"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.
[7]"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.
[8]"Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III."
Guenther B., Onrust R., Sali A., O'Donnell M., Kuriyan J.
Cell 91:335-345(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L04577 Genomic DNA. Translation: AAA23708.1.
L01483 Genomic DNA. Translation: AAA23696.1.
U00096 Genomic DNA. Translation: AAC74183.1.
AP009048 Genomic DNA. Translation: BAA35906.1.
PIRS35523.
RefSeqNP_415617.1. NC_000913.3.
YP_489367.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1A5TX-ray2.20A1-334[»]
1JR3X-ray2.70E1-334[»]
1XXHX-ray3.45E/J1-334[»]
1XXIX-ray4.10E/J1-334[»]
3GLFX-ray3.39E/J1-334[»]
3GLGX-ray3.25E/J1-334[»]
3GLHX-ray3.89E/J/O1-334[»]
3GLIX-ray3.50E/J1-334[»]
ProteinModelPortalP28631.
SMRP28631. Positions 1-334.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9932N.
IntActP28631. 25 interactions.
MINTMINT-1239429.
STRING511145.b1099.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74183; AAC74183; b1099.
BAA35906; BAA35906; BAA35906.
GeneID12934122.
945661.
KEGGecj:Y75_p1069.
eco:b1099.
PATRIC32117439. VBIEscCol129921_1142.

Organism-specific databases

EchoBASEEB1463.
EcoGeneEG11500. holB.

Phylogenomic databases

eggNOGCOG0470.
HOGENOMHOG000192595.
KOK02341.
OMACHSCHLM.
OrthoDBEOG6W9X5M.
PhylomeDBP28631.
ProtClustDBPRK07993.

Enzyme and pathway databases

BioCycEcoCyc:EG11500-MONOMER.
ECOL316407:JW1085-MONOMER.

Gene expression databases

GenevestigatorP28631.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR004622. DNA_pol_HolB.
IPR015199. DNA_pol_III_delta_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF09115. DNApol3-delta_C. 1 hit.
[Graphical view]
SUPFAMSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00678. holB. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP28631.
PROP28631.

Entry information

Entry nameHOLB_ECOLI
AccessionPrimary (citable) accession number: P28631
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 132 of the entry and version 2 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