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Protein

DNA polymerase III subunit delta'

Gene

holB

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.

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

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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11500. holB.

Subcellular locationi

GO - Cellular componenti

  1. DNA polymerase III complex Source: EcoCyc
  2. DNA replication factor C complex Source: GO_Central
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

1
334
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 73Combined sources
Helixi8 – 1912Combined sources
Beta strandi25 – 306Combined sources
Helixi37 – 4812Combined sources
Beta strandi55 – 573Combined sources
Helixi63 – 708Combined sources
Beta strandi76 – 794Combined sources
Beta strandi86 – 883Combined sources
Helixi90 – 9910Combined sources
Beta strandi110 – 1156Combined sources
Helixi117 – 1193Combined sources
Helixi122 – 13211Combined sources
Beta strandi139 – 1468Combined sources
Helixi148 – 1503Combined sources
Helixi153 – 1564Combined sources
Beta strandi159 – 1635Combined sources
Helixi169 – 17911Combined sources
Helixi184 – 19310Combined sources
Turni194 – 1963Combined sources
Helixi198 – 2036Combined sources
Helixi208 – 22619Combined sources
Helixi230 – 2323Combined sources
Helixi233 – 2364Combined sources
Helixi241 – 25515Combined sources
Turni259 – 2613Combined sources
Helixi271 – 28010Combined sources
Helixi283 – 30321Combined sources
Helixi308 – 32215Combined sources
Beta strandi324 – 3263Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
SMRiP28631. Positions 1-334.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28631.

Family & Domainsi

Phylogenomic databases

eggNOGiCOG0470.
HOGENOMiHOG000192595.
InParanoidiP28631.
KOiK02341.
OMAiTYFLLGC.
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

        10         20         30         40         50
MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC
60 70 80 90 100
QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL
110 120 130 140 150
NEHARLGGAK VVWVTDAALL TDAAANALLK TLEEPPAETW FFLATREPER
160 170 180 190 200
LLATLRSRCR LHYLAPPPEQ YAVTWLSREV TMSQDALLAA LRLSAGSPGA
210 220 230 240 250
ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ APARLHWLAT
260 270 280 290 300
LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL
310 320 330
MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL
Length:334
Mass (Da):36,937
Last modified:November 1, 1997 - v2
Checksum:iDC9DAA644AD8A096
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti166 – 1661P → G in AAA23708 (PubMed:8505303).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
SMRiP28631. Positions 1-334.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB1463.
EcoGeneiEG11500. holB.

Phylogenomic databases

eggNOGiCOG0470.
HOGENOMiHOG000192595.
InParanoidiP28631.
KOiK02341.
OMAiTYFLLGC.
OrthoDBiEOG6W9X5M.
PhylomeDBiP28631.

Enzyme and pathway databases

BioCyciEcoCyc:EG11500-MONOMER.
ECOL316407:JW1085-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP28631.
PROiP28631.

Gene expression databases

GenevestigatoriP28631.

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.
ProtoNetiSearch...

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: March 4, 2015
This is version 140 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

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 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.