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Protein

DNA polymerase III subunit delta

Gene

holA

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'-5' exonuclease activity. The delta subunit is the wrench that will open the beta subunit dimer, which has been modeled to leave a gap large enough for ssDNA to pass through (PubMed:11525728). 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).1 Publication2 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:EG11412-MONOMER
MetaCyc:EG11412-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase III subunit delta (EC:2.7.7.7)
Gene namesi
Name:holA
Ordered Locus Names:b0640, JW0635
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11412 holA

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001055051 – 343DNA polymerase III subunit deltaAdd BLAST343

Proteomic databases

PaxDbiP28630
PRIDEiP28630

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

BioGridi4259908, 201 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
DIPiDIP-9931N
IntActiP28630, 49 interactors
STRINGi316385.ECDH10B_0709

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP28630
SMRiP28630
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28630

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 140Domain 11 PublicationAdd BLAST140
Regioni141 – 210Domain 21 PublicationAdd BLAST70
Regioni211 – 343Domain 31 PublicationAdd BLAST133

Domaini

Has three domains, each of which is closely related to a corresponding domain in the delta' stator, despite the 2 proteins having only 6-8% sequence identity. Interacts with the beta sliding clamp via domain 1 (residues 1-140, in particular residues 61-74), fitting into a cleft between domains 2 and 3 on the surface of the beta-clamp (PubMed:11525728). Residues 61-74 move about 45 degrees and 5.5 Angstroms in the beta-delta versus gamma-delta-delta' structure to contact respectively the beta or delta' (PubMed:11525728).1 Publication

Phylogenomic databases

eggNOGiENOG4105DJF Bacteria
COG1466 LUCA
HOGENOMiHOG000256204
InParanoidiP28630
KOiK02340
OMAiRIPTGKP
PhylomeDBiP28630

Family and domain databases

InterProiView protein in InterPro
IPR008921 DNA_pol3_clamp-load_cplx_C
IPR032780 DNA_pol3_delt_C
IPR010372 DNA_pol3_delta_N
IPR005790 DNA_polIII_delta
IPR027417 P-loop_NTPase
PfamiView protein in Pfam
PF14840 DNA_pol3_delt_C, 1 hit
PF06144 DNA_pol3_delta, 1 hit
SUPFAMiSSF48019 SSF48019, 1 hit
SSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR01128 holA, 1 hit

Sequencei

Sequence statusi: Complete.

P28630-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH
60 70 80 90 100
HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL
110 120 130 140 150
TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW
160 170 180 190 200
VAARAKQLNL ELDDAANQVL CYCYEGNLLA LAQALERLSL LWPDGKLTLP
210 220 230 240 250
RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG SEPVILLRTL
260 270 280 290 300
QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ
310 320 330 340
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG
Length:343
Mass (Da):38,704
Last modified:December 1, 1992 - v1
Checksum:i87239A678FE16BE2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04576 Genomic DNA Translation: AAA23675.1
M94267 Genomic DNA Translation: AAB59047.1
U82598 Genomic DNA Translation: AAB40841.1
U00096 Genomic DNA Translation: AAC73741.1
AP009048 Genomic DNA Translation: BAA35287.1
M18277 Genomic DNA No translation available.
PIRiA45251
RefSeqiNP_415173.1, NC_000913.3
WP_000620535.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640
BAA35287; BAA35287; BAA35287
GeneIDi947573
KEGGiecj:JW0635
eco:b0640
PATRICifig|1411691.4.peg.1628

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04576 Genomic DNA Translation: AAA23675.1
M94267 Genomic DNA Translation: AAB59047.1
U82598 Genomic DNA Translation: AAB40841.1
U00096 Genomic DNA Translation: AAC73741.1
AP009048 Genomic DNA Translation: BAA35287.1
M18277 Genomic DNA No translation available.
PIRiA45251
RefSeqiNP_415173.1, NC_000913.3
WP_000620535.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90C/D1-343[»]
1JQLX-ray2.50B1-140[»]
1JR3X-ray2.70D1-343[»]
1XXHX-ray3.45A/F1-343[»]
1XXIX-ray4.10A/F1-343[»]
3GLFX-ray3.39A/F1-343[»]
3GLGX-ray3.25A/F1-343[»]
3GLHX-ray3.89A/F/K1-343[»]
3GLIX-ray3.50A/F1-343[»]
ProteinModelPortaliP28630
SMRiP28630
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259908, 201 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
DIPiDIP-9931N
IntActiP28630, 49 interactors
STRINGi316385.ECDH10B_0709

Proteomic databases

PaxDbiP28630
PRIDEiP28630

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640
BAA35287; BAA35287; BAA35287
GeneIDi947573
KEGGiecj:JW0635
eco:b0640
PATRICifig|1411691.4.peg.1628

Organism-specific databases

EchoBASEiEB1384
EcoGeneiEG11412 holA

Phylogenomic databases

eggNOGiENOG4105DJF Bacteria
COG1466 LUCA
HOGENOMiHOG000256204
InParanoidiP28630
KOiK02340
OMAiRIPTGKP
PhylomeDBiP28630

Enzyme and pathway databases

BioCyciEcoCyc:EG11412-MONOMER
MetaCyc:EG11412-MONOMER

Miscellaneous databases

EvolutionaryTraceiP28630
PROiPR:P28630

Family and domain databases

InterProiView protein in InterPro
IPR008921 DNA_pol3_clamp-load_cplx_C
IPR032780 DNA_pol3_delt_C
IPR010372 DNA_pol3_delta_N
IPR005790 DNA_polIII_delta
IPR027417 P-loop_NTPase
PfamiView protein in Pfam
PF14840 DNA_pol3_delt_C, 1 hit
PF06144 DNA_pol3_delta, 1 hit
SUPFAMiSSF48019 SSF48019, 1 hit
SSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR01128 holA, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiHOLA_ECOLI
AccessioniPrimary (citable) accession number: P28630
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: June 20, 2018
This is version 154 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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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