SubmitCancel

Skip Header

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

P28631

- HOLB_ECOLI

UniProt

P28631 - HOLB_ECOLI

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein
DNA polymerase III subunit delta'
Gene
holB, b1099, JW1085
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.

Catalytic activityi

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

GO - Molecular functioni

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

GO - Biological processi

  1. 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:EG11500-MONOMER.
ECOL316407:JW1085-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase III subunit delta' (EC:2.7.7.7)
Gene namesi
Name:holB
Ordered Locus Names:b1099, JW1085
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11500. holB.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 334334DNA polymerase III subunit delta'
PRO_0000105513Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP28631.

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
dnaXP0671017EBI-549161,EBI-549140
dnaXP06710-16EBI-549161,EBI-6464728
holAP2863017EBI-549161,EBI-549153
holCP289055EBI-549161,EBI-549169
mutLP233672EBI-549161,EBI-554913

Protein-protein interaction databases

DIPiDIP-9932N.
IntActiP28631. 25 interactions.
MINTiMINT-1239429.
STRINGi511145.b1099.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 73
Helixi8 – 1912
Beta strandi25 – 306
Helixi37 – 4812
Beta strandi55 – 573
Helixi63 – 708
Beta strandi76 – 794
Beta strandi86 – 883
Helixi90 – 9910
Beta strandi110 – 1156
Helixi117 – 1193
Helixi122 – 13211
Beta strandi139 – 1468
Helixi148 – 1503
Helixi153 – 1564
Beta strandi159 – 1635
Helixi169 – 17911
Helixi184 – 19310
Turni194 – 1963
Helixi198 – 2036
Helixi208 – 22619
Helixi230 – 2323
Helixi233 – 2364
Helixi241 – 25515
Turni259 – 2613
Helixi271 – 28010
Helixi283 – 30321
Helixi308 – 32215
Beta strandi324 – 3263

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP28631.

Miscellaneous databases

EvolutionaryTraceiP28631.

Family & Domainsi

Phylogenomic databases

eggNOGiCOG0470.
HOGENOMiHOG000192595.
KOiK02341.
OMAiCHSCHLM.
OrthoDBiEOG6W9X5M.
PhylomeDBiP28631.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR004622. DNA_pol_HolB.
IPR015199. DNA_pol_III_delta_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF09115. DNApol3-delta_C. 1 hit.
[Graphical view]
SUPFAMiSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00678. holB. 1 hit.

Sequencei

Sequence statusi: Complete.

P28631-1 [UniParc]FASTAAdd to Basket

« Hide

MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC    50
QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL 100
NEHARLGGAK VVWVTDAALL TDAAANALLK TLEEPPAETW FFLATREPER 150
LLATLRSRCR LHYLAPPPEQ YAVTWLSREV TMSQDALLAA LRLSAGSPGA 200
ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ APARLHWLAT 250
LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL 300
MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL 334
Length:334
Mass (Da):36,937
Last modified:November 1, 1997 - v2
Checksum:iDC9DAA644AD8A096
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti166 – 1661P → G in AAA23708. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L04577 Genomic DNA. Translation: AAA23708.1.
L01483 Genomic DNA. Translation: AAA23696.1.
U00096 Genomic DNA. Translation: AAC74183.1.
AP009048 Genomic DNA. Translation: BAA35906.1.
PIRiS35523.
RefSeqiNP_415617.1. NC_000913.3.
YP_489367.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74183; AAC74183; b1099.
BAA35906; BAA35906; BAA35906.
GeneIDi12934122.
945661.
KEGGiecj:Y75_p1069.
eco:b1099.
PATRICi32117439. VBIEscCol129921_1142.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L04577 Genomic DNA. Translation: AAA23708.1 .
L01483 Genomic DNA. Translation: AAA23696.1 .
U00096 Genomic DNA. Translation: AAC74183.1 .
AP009048 Genomic DNA. Translation: BAA35906.1 .
PIRi S35523.
RefSeqi NP_415617.1. NC_000913.3.
YP_489367.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1A5T X-ray 2.20 A 1-334 [» ]
1JR3 X-ray 2.70 E 1-334 [» ]
1XXH X-ray 3.45 E/J 1-334 [» ]
1XXI X-ray 4.10 E/J 1-334 [» ]
3GLF X-ray 3.39 E/J 1-334 [» ]
3GLG X-ray 3.25 E/J 1-334 [» ]
3GLH X-ray 3.89 E/J/O 1-334 [» ]
3GLI X-ray 3.50 E/J 1-334 [» ]
ProteinModelPortali P28631.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9932N.
IntActi P28631. 25 interactions.
MINTi MINT-1239429.
STRINGi 511145.b1099.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74183 ; AAC74183 ; b1099 .
BAA35906 ; BAA35906 ; BAA35906 .
GeneIDi 12934122.
945661.
KEGGi ecj:Y75_p1069.
eco:b1099.
PATRICi 32117439. VBIEscCol129921_1142.

Organism-specific databases

EchoBASEi EB1463.
EcoGenei EG11500. holB.

Phylogenomic databases

eggNOGi COG0470.
HOGENOMi HOG000192595.
KOi K02341.
OMAi CHSCHLM.
OrthoDBi EOG6W9X5M.
PhylomeDBi P28631.

Enzyme and pathway databases

BioCyci EcoCyc:EG11500-MONOMER.
ECOL316407:JW1085-MONOMER.

Miscellaneous databases

EvolutionaryTracei P28631.
PROi P28631.

Gene expression databases

Genevestigatori P28631.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
InterProi IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR004622. DNA_pol_HolB.
IPR015199. DNA_pol_III_delta_C.
IPR027417. P-loop_NTPase.
[Graphical view ]
Pfami PF09115. DNApol3-delta_C. 1 hit.
[Graphical view ]
SUPFAMi SSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR00678. holB. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. 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).

Entry informationi

Entry nameiHOLB_ECOLI
AccessioniPrimary (citable) accession number: P28631
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: November 1, 1997
Last modified: June 11, 2014
This is version 134 of the entry and version 2 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