P28630 (HOLA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA polymerase III subunit delta
EC=2.7.7.7

Gene names

Name:	holA
Ordered Locus Names:	b0640, JW0635

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	343 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Subunit structure	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].

Ontologies

Keywords
Biological process	DNA replication
Molecular function	DNA-directed DNA polymerase Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent DNA replication Inferred from direct assay PubMed 10924523. Source: EcoCyc
Cellular_component	DNA polymerase III complex Inferred from direct assay PubMed 7768937. Source: EcoCyc
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaN	P0A988	9	EBI-549153,EBI-542385
dnaX	P06710-1	5	EBI-549153,EBI-6464728
holB	P28631	16	EBI-549153,EBI-549161
mutL	P23367	2	EBI-549153,EBI-554913

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 343

343

DNA polymerase III subunit delta

PRO_0000105505

Secondary structure

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343

Helix Strand Turn

Details...

Beta strand

2 – 4

3

Helix

6 – 8

3

Helix

9 – 15

7

Beta strand

19 – 26

8

Helix

28 – 44

17

Beta strand

49 – 51

3

Helix

61 – 69

9

Beta strand

73 – 76

4

Beta strand

78 – 83

6

Helix

93 – 103

11

Beta strand

106 – 108

3

Beta strand

110 – 113

4

Helix

121 – 123

3

Helix

125 – 130

6

Helix

131 – 133

3

Beta strand

135 – 138

4

Turn

144 – 146

3

Helix

147 – 156

10

Turn

157 – 159

3

Helix

164 – 174

11

Helix

178 – 191

14

Helix

199 – 206

8

Helix

214 – 222

9

Helix

226 – 235

10

Turn

236 – 240

5

Turn

243 – 245

3

Helix

246 – 261

16

Turn

262 – 266

5

Turn

269 – 275

7

Helix

280 – 282

3

Turn

283 – 285

3

Helix

286 – 292

7

Helix

295 – 314

20

Helix

325 – 331

7

Sequences

	Sequence		Length	Mass (Da)
	P28630 [UniParc]. Last modified December 1, 1992. Version 1. Checksum: 87239A678FE16BE2	FASTA	343	38,704
	10 20 30 40 50 60 MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD 70 80 90 100 110 120 WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA 130 140 150 160 170 180 QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL CYCYEGNLLA 190 200 210 220 230 240 LAQALERLSL LWPDGKLTLP RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG 250 260 270 280 290 300 SEPVILLRTL QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ 310 320 330 340 AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] 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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

A45251.

RefSeq

NP_415173.1. NC_000913.2.
YP_488931.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P28630.

SMR

P28630. Positions 1-338.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9931N.

IntAct

P28630. 27 interactions.

MINT

MINT-1235044.

STRING

511145.b0640.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73741; AAC73741; b0640.
BAA35287; BAA35287; BAA35287.

GeneID

12930914.
947573.

KEGG

ecj:Y75_p0630.
eco:b0640.

PATRIC

32116463. VBIEscCol129921_0671.

Organism-specific databases

EchoBASE

EB1384.

EcoGene

EG11412. holA.

Phylogenomic databases

eggNOG

COG1466.

HOGENOM

HOG000256204.

KO

K02340.

OMA

FGDDPWL.

ProtClustDB

PRK05574.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P28630.

Family and domain databases

InterPro

IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR010372. DNA_pol3_delta.
IPR005790. DNA_polIII_delta.
[Graphical view]

Pfam

PF06144. DNA_pol3_delta. 1 hit.
[Graphical view]

SUPFAM

SSF48019. Pol_clamp_load_C. 1 hit.

TIGRFAMs

TIGR01128. holA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P28630.

Entry information

Entry name

HOLA_ECOLI

Accession

Primary (citable) accession number: P28630

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	May 1, 2013
This is version 121 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program