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P28630

- HOLA_ECOLI

UniProt

P28630 - HOLA_ECOLI

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Protein

DNA polymerase III subunit delta

Gene

holA

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. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA.

Catalytic activityi

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

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. 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:EG11412-MONOMER.
ECOL316407:JW0635-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11412. holA.

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 – 343343DNA polymerase III subunit deltaPRO_0000105505Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP28630.

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
dnaEP104434EBI-549153,EBI-549111
dnaNP0A98810EBI-549153,EBI-542385
dnaXP06710-15EBI-549153,EBI-6464728
holBP2863117EBI-549153,EBI-549161
mutLP233672EBI-549153,EBI-554913
nfsAP171173EBI-549153,EBI-1120624
yeeWP645262EBI-549153,EBI-9146863

Protein-protein interaction databases

DIPiDIP-9931N.
IntActiP28630. 49 interactions.
MINTiMINT-1235044.
STRINGi511145.b0640.

Structurei

Secondary structure

1
343
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Helixi6 – 83Combined sources
Helixi9 – 157Combined sources
Beta strandi19 – 268Combined sources
Helixi28 – 4417Combined sources
Beta strandi49 – 513Combined sources
Helixi61 – 699Combined sources
Beta strandi73 – 764Combined sources
Beta strandi78 – 836Combined sources
Helixi93 – 10311Combined sources
Beta strandi106 – 1083Combined sources
Beta strandi110 – 1134Combined sources
Helixi121 – 1233Combined sources
Helixi125 – 1306Combined sources
Helixi131 – 1333Combined sources
Beta strandi135 – 1384Combined sources
Turni144 – 1463Combined sources
Helixi147 – 15610Combined sources
Turni157 – 1593Combined sources
Helixi164 – 17411Combined sources
Helixi178 – 19114Combined sources
Helixi199 – 2068Combined sources
Helixi214 – 2229Combined sources
Helixi226 – 23510Combined sources
Turni236 – 2405Combined sources
Turni243 – 2453Combined sources
Helixi246 – 26116Combined sources
Turni262 – 2665Combined sources
Turni269 – 2757Combined sources
Helixi280 – 2823Combined sources
Turni283 – 2853Combined sources
Helixi286 – 2927Combined sources
Helixi295 – 31420Combined sources
Helixi325 – 3317Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-338.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28630.

Family & Domainsi

Phylogenomic databases

eggNOGiCOG1466.
HOGENOMiHOG000256204.
InParanoidiP28630.
KOiK02340.
OMAiQHRVWQN.
OrthoDBiEOG6BCSPJ.
PhylomeDBiP28630.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
IPR010372. DNA_pol3_delta.
IPR005790. DNA_polIII_delta.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF06144. DNA_pol3_delta. 1 hit.
[Graphical view]
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.
YP_488931.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640.
BAA35287; BAA35287; BAA35287.
GeneIDi12930914.
947573.
KEGGiecj:Y75_p0630.
eco:b0640.
PATRICi32116463. VBIEscCol129921_0671.

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.
PIRi A45251.
RefSeqi NP_415173.1. NC_000913.3.
YP_488931.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1JQJ X-ray 2.90 C/D 1-343 [» ]
1JQL X-ray 2.50 B 1-140 [» ]
1JR3 X-ray 2.70 D 1-343 [» ]
1XXH X-ray 3.45 A/F 1-343 [» ]
1XXI X-ray 4.10 A/F 1-343 [» ]
3GLF X-ray 3.39 A/F 1-343 [» ]
3GLG X-ray 3.25 A/F 1-343 [» ]
3GLH X-ray 3.89 A/F/K 1-343 [» ]
3GLI X-ray 3.50 A/F 1-343 [» ]
ProteinModelPortali P28630.
SMRi P28630. Positions 1-338.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9931N.
IntActi P28630. 49 interactions.
MINTi MINT-1235044.
STRINGi 511145.b0640.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73741 ; AAC73741 ; b0640 .
BAA35287 ; BAA35287 ; BAA35287 .
GeneIDi 12930914.
947573.
KEGGi ecj:Y75_p0630.
eco:b0640.
PATRICi 32116463. VBIEscCol129921_0671.

Organism-specific databases

EchoBASEi EB1384.
EcoGenei EG11412. holA.

Phylogenomic databases

eggNOGi COG1466.
HOGENOMi HOG000256204.
InParanoidi P28630.
KOi K02340.
OMAi QHRVWQN.
OrthoDBi EOG6BCSPJ.
PhylomeDBi P28630.

Enzyme and pathway databases

BioCyci EcoCyc:EG11412-MONOMER.
ECOL316407:JW0635-MONOMER.

Miscellaneous databases

EvolutionaryTracei P28630.
PROi P28630.

Gene expression databases

Genevestigatori P28630.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
InterProi IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR010372. DNA_pol3_delta.
IPR005790. DNA_polIII_delta.
IPR027417. P-loop_NTPase.
[Graphical view ]
Pfami PF06144. DNA_pol3_delta. 1 hit.
[Graphical view ]
SUPFAMi SSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR01128. holA. 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. "Molecular cloning, sequencing, and overexpression 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. 174:7013-7025(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "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.
  7. "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome."
    Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H., Ohta T., Matsuhashi M.
    J. Bacteriol. 169:5692-5699(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
    Strain: K12.
  8. "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.
  9. "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.
  10. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.

Entry informationi

Entry nameiHOLA_ECOLI
AccessioniPrimary (citable) accession number: P28630
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: November 26, 2014
This is version 132 of the entry and version 1 of the sequence. [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. 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