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Protein

DNA polymerase III subunit delta'

Gene

holB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

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

Protein-protein interaction databases

BioGridi4263116, 181 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
DIPiDIP-9932N
IntActiP28631, 25 interactors
STRINGi316385.ECDH10B_1171

Structurei

Secondary structure

1334
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP28631
SMRiP28631
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28631

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4107QRG Bacteria
COG0470 LUCA
HOGENOMiHOG000192595
InParanoidiP28631
KOiK02341
OMAiQRGHAWL
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

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
WP_001267956.1, NZ_LN832404.1

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...

Protein-protein interaction databases

BioGridi4263116, 181 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
DIPiDIP-9932N
IntActiP28631, 25 interactors
STRINGi316385.ECDH10B_1171

Proteomic databases

PaxDbiP28631
PRIDEiP28631

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB1463
EcoGeneiEG11500 holB

Phylogenomic databases

eggNOGiENOG4107QRG Bacteria
COG0470 LUCA
HOGENOMiHOG000192595
InParanoidiP28631
KOiK02341
OMAiQRGHAWL
PhylomeDBiP28631

Enzyme and pathway databases

BioCyciEcoCyc:EG11500-MONOMER
MetaCyc:EG11500-MONOMER

Miscellaneous databases

EvolutionaryTraceiP28631
PROiPR:P28631

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
ProtoNetiSearch...

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: June 20, 2018
This is version 161 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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Main funding by: National Institutes of Health

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