DNA polymerase III subunit epsilon - Escherichia coli (strain K12)

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P03007 (DPO3E_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 134. 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 epsilon
EC=2.7.7.7

Gene names

Name:	dnaQ
Synonyms:	mutD
Ordered Locus Names:	b0215, JW0205

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	243 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. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Cofactor	Binds 2 divalent metal cations. Magnesium or manganese.
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].
Sequence caution	The sequence AAB08637.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	DNA replication
Ligand	Magnesium Manganese Metal-binding
Molecular function	DNA-directed DNA polymerase Exonuclease Hydrolase Nuclease Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication proofreading Inferred from mutant phenotype PubMed 6340117. Source: EcoCyc
Cellular_component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW exonuclease activity Inferred from direct assay PubMed 6393125. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaE	P10443	11	EBI-549131,EBI-549111
holE	P0ABS8	6	EBI-549131,EBI-549182

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 243

243

DNA polymerase III subunit epsilon

PRO_0000105483

Sites

Active site

162

Proton acceptor

Metal binding

Divalent metal cation 1; catalytic

Metal binding

Divalent metal cation 2; catalytic

Metal binding

Divalent metal cation 1; catalytic

Metal binding

167

Divalent metal cation 1; catalytic

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

167

Substrate

Secondary structure

243

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P03007 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: 4211C9A00744964F
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FASTA

243

27,099

        10         20         30         40         50         60 
MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVVN RRLTGNNFHV YLKPDRLVDP 

        70         80         90        100        110        120 
EAFGVHGIAD EFLLDKPTFA EVADEFMDYI RGAELVIHNA AFDIGFMDYE FSLLKRDIPK 

       130        140        150        160        170        180 
TNTFCKVTDS LAVARKMFPG KRNSLDALCA RYEIDNSKRT LHGALLDAQI LAEVYLAMTG 

       190        200        210        220        230        240 
GQTSMAFAME GETQQQQGEA TIQRIVRQAS KLRVVFATDE EIAAHEARLD LVQKKGGSCL 


WRA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia coli mutator gene." Cox E.C., Horner D.L. J. Mol. Biol. 190:113-117(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions." Maki H., Horiuchi T., Sekiguchi M. Proc. Natl. Acad. Sci. U.S.A. 80:7137-7141(1983) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Structure and function of dnaQ and mutD mutators of Escherichia coli." Takano K., Nakabeppu Y., Maki H., Horiuchi T., Sekiguchi M. Mol. Gen. Genet. 205:9-13(1986) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region." Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"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.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"Structural basis for proofreading during replication of the Escherichia coli chromosome." Hamdan S., Carr P.D., Brown S.E., Ollis D.L., Dixon N.E. Structure 10:535-546(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-186 IN COMPLEX WITH METAL IONS AND SUBSTRATE ANALOG.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X04027 Genomic DNA. Translation: CAA27661.1.
K00985 Genomic DNA. Translation: AAA24564.1.
U70214 Genomic DNA. Translation: AAB08637.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73320.1.
AP009048 Genomic DNA. Translation: BAA77886.1.

PIR

IQECQ. A64746.

RefSeq

NP_414751.1. NC_000913.2.
YP_488512.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J53	X-ray	1.80	A	1-186	[»]
1J54	X-ray	1.70	A	1-186	[»]
1MGZ	model	-	A	1-186	[»]
2GUI	X-ray	1.60	A	2-186	[»]
2IDO	X-ray	2.10	A/C	1-186	[»]
2XY8	NMR	-	A	1-186	[»]

ProteinModelPortal

P03007.

SMR

P03007. Positions 5-180.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9462N.

IntAct

P03007. 26 interactions.

MINT

MINT-1222832.

STRING

511145.b0215.

2D gel databases

SWISS-2DPAGE

P03007.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73320; AAC73320; b0215.
BAA77886; BAA77886; BAA77886.

GeneID

12933127.
946441.

KEGG

ecj:Y75_p0206.
eco:b0215.

PATRIC

32115543. VBIEscCol129921_0217.

Organism-specific databases

EchoBASE

EB0239.

EcoGene

EG10243. dnaQ.

Phylogenomic databases

eggNOG

COG0847.

HOGENOM

HOG000258616.

K02342.

OMA

HGITNEF.

ProtClustDB

PRK05711.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10243-MONOMER.
ECOL316407:JW0205-MONOMER.
MetaCyc:EG10243-MONOMER.

Gene expression databases

Genevestigator

P03007.

Family and domain databases

InterPro

IPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR006055. Exonuclease.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]

Pfam

PF00929. RNase_T. 1 hit.
[Graphical view]

SMART

SM00479. EXOIII. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

TIGRFAMs

TIGR00573. dnaq. 1 hit.
TIGR01406. dnaQ_proteo. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1075047.

EvolutionaryTrace

P03007.

Entry information

Entry name

DPO3E_ECOLI

Accession

Primary (citable) accession number: P03007

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	April 1, 1988
Last modified:	May 1, 2013
This is version 134 of the entry and version 1 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

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents