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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

Part of the beta sliding clamp loading complex, which hydrolyzes ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex (PubMed:2040637). 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 gamma complex (gamma3,delta,delta') is thought to load beta dimers onto DNA by binding ATP which alters the complex's conformation so it can bind beta sliding clamp dimers and open them at one interface. Primed DNA is recognized, ATP is hydrolyzed releasing the gamma complex and closing the beta sliding clamp ring around the primed DNA (PubMed:9927437).2 Publications

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

  • DNA-dependent DNA replication Source: EcoCyc

Keywordsi

Molecular functionDNA-directed DNA polymerase, Nucleotidyltransferase, Transferase
Biological processDNA replication

Enzyme and pathway databases

BioCyciEcoCyc:EG11500-MONOMER.
MetaCyc:EG11500-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11500. holB.

Subcellular locationi

GO - Cellular componenti

  • DNA polymerase III complex Source: EcoCyc

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001055131 – 334DNA polymerase III subunit delta'Add BLAST334

Proteomic databases

PaxDbiP28631.
PRIDEiP28631.

Interactioni

Subunit structurei

The DNA polymerase III holoenzyme complex contains at least 10 different subunits 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 (PubMed:2040637). The polymerase is tethered to the template via the dimeric beta sliding clamp processivity factor. The clamp-loading complex (also called gamma complex) assembles the beta sliding clamp onto the primed template and plays a central role in the organization and communication at the replication fork. The clamp-loading complex contains delta, delta', psi and chi, and 3 copies of either or both of two different DnaX proteins, gamma and tau. The DNA replisome complex has a single clamp loader (3 tau and 1 each of delta, delta', psi and chi subunits) which binds 3 Pol III cores (1 core on the leading strand and 2 on the lagging strand) each with a beta sliding clamp dimer. Additional proteins in the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase (PubMed:20413500, PubMed:22157955). The clamp loader hydrolyzes ATP to assemble the beta processivity factor onto the primed template (PubMed:2040637, PubMed:9927437) and plays a central role in the organization and communication at the replication fork; the minimal complex to load the beta sliding clamp on DNA is delta, delta', gamma (PubMed:9927437).5 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4263116. 175 interactors.
DIPiDIP-9932N.
IntActiP28631. 25 interactors.
MINTiMINT-1239429.
STRINGi316385.ECDH10B_1171.

Structurei

Secondary structure

1334
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 7Combined sources3
Helixi8 – 19Combined sources12
Beta strandi25 – 30Combined sources6
Helixi37 – 48Combined sources12
Beta strandi55 – 57Combined sources3
Helixi63 – 70Combined sources8
Beta strandi76 – 79Combined sources4
Beta strandi86 – 88Combined sources3
Helixi90 – 99Combined sources10
Beta strandi110 – 115Combined sources6
Helixi117 – 119Combined sources3
Helixi122 – 132Combined sources11
Beta strandi139 – 146Combined sources8
Helixi148 – 150Combined sources3
Helixi153 – 156Combined sources4
Beta strandi159 – 163Combined sources5
Helixi169 – 179Combined sources11
Helixi184 – 193Combined sources10
Turni194 – 196Combined sources3
Helixi198 – 203Combined sources6
Helixi208 – 226Combined sources19
Helixi230 – 232Combined sources3
Helixi233 – 236Combined sources4
Helixi241 – 255Combined sources15
Turni259 – 261Combined sources3
Helixi271 – 280Combined sources10
Helixi283 – 303Combined sources21
Helixi308 – 322Combined sources15
Beta strandi324 – 326Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28631.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4107QRG. Bacteria.
COG0470. LUCA.
HOGENOMiHOG000192595.
InParanoidiP28631.
KOiK02341.
PhylomeDBiP28631.

Family and domain databases

InterProiView protein in InterPro
IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR004622. DNA_pol_HolB.
IPR015199. DNA_pol_III_delta_C.
IPR027417. P-loop_NTPase.
PfamiView protein in Pfam
PF09115. DNApol3-delta_C. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti166P → G in AAA23708 (PubMed:8505303).Curated1

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.
WP_001267956.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74183; AAC74183; b1099.
BAA35906; BAA35906; BAA35906.
GeneIDi945661.
KEGGiecj:JW1085.
eco:b1099.
PATRICifig|1411691.4.peg.1169.

Similar proteinsi

Entry informationi

Entry nameiHOLB_ECOLI
AccessioniPrimary (citable) accession number: P28631
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: November 1, 1997
Last modified: October 25, 2017
This is version 158 of the entry and version 2 of the sequence. See 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