DNA polymerase III subunit delta' - Escherichia coli (strain K12)

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P28631 (HOLB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 113. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA polymerase III subunit delta'
EC=2.7.7.7

Gene names

Name:	holB
Ordered Locus Names:	b1099, JW1085

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	334 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.
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 Reference proteome
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	DNA polymerase III complex Inferred from electronic annotation. Source: InterPro
Molecular function	3'-5' exonuclease activity Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
mutL	P23367	2	EBI-549161,EBI-554913

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 334

334

DNA polymerase III subunit delta'

PRO_0000105513

Experimental info

Sequence conflict

166

P → G in AAA23708. Ref.1

Secondary structure

334

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P28631 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: DC9DAA644AD8A096
Show »

FASTA

334

36,937

        10         20         30         40         50         60 
MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG 

        70         80         90        100        110        120 
HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL NEHARLGGAK VVWVTDAALL 

       130        140        150        160        170        180 
TDAAANALLK TLEEPPAETW FFLATREPER LLATLRSRCR LHYLAPPPEQ YAVTWLSREV 

       190        200        210        220        230        240 
TMSQDALLAA LRLSAGSPGA ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ 

       250        260        270        280        290        300 
APARLHWLAT LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL 

       310        320        330 
MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL

« Hide

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: 8505303] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Identification, isolation, and characterization 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. 175:3812-3822(1993) [PubMed: 8509334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. 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. Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"DNA polymerase III accessory proteins. II. Characterization of delta and delta'." Onrust R., O'Donnell M. J. Biol. Chem. 268:11766-11772(1993) [PubMed: 8505304] [Abstract] Cited for: CHARACTERIZATION.
[7]	"Accessory protein function in the DNA polymerase III holoenzyme from E. coli." O'Donnell M. Bioessays 14:105-111(1992) [PubMed: 1575709] [Abstract] Cited for: REVIEW.
[8]	"Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III." Guenther B., Onrust R., Sali A., O'Donnell M., Kuriyan J. Cell 91:335-345(1997) [PubMed: 9363942] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L04577 Genomic DNA. Translation: AAA23708.1.
L01483 Genomic DNA. Translation: AAA23696.1.
U00096 Genomic DNA. Translation: AAC74183.1.
AP009048 Genomic DNA. Translation: BAA35906.1.

PIR

S35523.

RefSeq

NP_415617.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A5T	X-ray	2.20	A	1-334	[»]
1JR3	X-ray	2.70	E	1-334	[»]
1XXH	X-ray	3.45	E/J	1-334	[»]
1XXI	X-ray	4.10	E/J	1-334	[»]
3GLF	X-ray	3.39	E/J	1-334	[»]
3GLG	X-ray	3.25	E/J	1-334	[»]
3GLH	X-ray	3.89	E/J/O	1-334	[»]
3GLI	X-ray	3.50	E/J	1-334	[»]

ProteinModelPortal

P28631.

SMR

P28631. Positions 1-334.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9932N.

IntAct

P28631. 23 interactions.

MINT

MINT-1239429.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003941; EBESCP00000003941; EBESCG00000003226.
EBESCT00000017474; EBESCP00000016765; EBESCG00000016530.

GeneID

945661.

GenomeReviews

Gene locus JW1085 in contig AP009048_GR.
Gene locus b1099 in contig U00096_GR.

KEGG

ecj:JW1085.
eco:b1099.

PATRIC

32117439. VBIEscCol129921_1142.

Organism-specific databases

EchoBASE

EB1463.

EcoGene

EG11500. holB.

Phylogenomic databases

eggNOG

COG0470.

GeneTree

EBGT00050000009793.

HOGENOM

HBG729459.

OMA

CHSCHLM.

PhylomeDB

P28631.

ProtClustDB

PRK07993.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11500-MONOMER.

Gene expression databases

Genevestigator

P28631.

Family and domain databases

InterPro

IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR004622. DNA_pol_HolB.
IPR015199. DNA_pol_III_delta_C.
[Graphical view]

K02341.

Pfam

PF09115. DNApol3-delta_C. 1 hit.
[Graphical view]

SUPFAM

SSF48019. Pol_clamp_load_C. 1 hit.

TIGRFAMs

TIGR00678. HolB. 1 hit.

ProtoNet

Search...

Entry information

Entry name

HOLB_ECOLI

Accession

Primary (citable) accession number: P28631

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	November 1, 1997
Last modified:	January 25, 2012
This is version 113 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents