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

Contribute

Send feedback

Read comments (0) or add your own

Reviewed, UniProtKB/Swiss-Prot P0A988 (DPO3B_ECOLI)

Last modified June 16, 2009. Version 42. History...

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

Documents (2) |

Third-party data |

Customize display

text xml rdf/xml gff fasta

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Hide | Top

Names and origin

Protein names

Recommended name:
DNA polymerase III subunit beta
EC=2.7.7.7

Gene names

Name:	dnaN
Ordered Locus Names:	b3701, JW3678

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Hide | Top

Protein attributes

Sequence length	366 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

Hide | Top

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 beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex 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]. The beta chain is a homodimer when not associated with the other components.
Subcellular location	Cytoplasm.

Hide | Top

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Cytoplasm
Molecular function	DNA-directed DNA polymerase Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
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...

Hide | Top

Binary interactions

With	Entry	#Exp.	IntAct
groL	P0A6F5	1	EBI-542385,EBI-543750
hda	P69931	1	EBI-542385,EBI-545453
holA	P28630	1	EBI-542385,EBI-549153
rpe	P0AG07	1	EBI-542385,EBI-546020
yajQ	P0A8E7	1	EBI-542385,EBI-370752
ybbN	P77395	1	EBI-542385,EBI-545297
yhbH	P0AFX0	1	EBI-542385,EBI-561113
zwf	P0AC53	1	EBI-542385,EBI-555656

Hide | Top

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 366

366

DNA polymerase III subunit beta

PRO_0000105434

Regions

Region

1 – 125

125

Region

126 – 253

128

Region

254 – 366

113

III

Secondary structure

366

Helix Strand Turn

Details...

Hide | Top

Sequences

Sequence

Length

Mass (Da)

Tools

P0A988-1 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: 7A45646F61255B5A
Show »

FASTA

366

40,587

        10         20         30         40         50         60 
MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV 

        70         80         90        100        110        120 
QPHEPGATTV PARKFFDICR GLPEGAEIAV QLEGERMLVR SGRSRFSLST LPAADFPNLD 

       130        140        150        160        170        180 
DWQSEVEFTL PQATMKRLIE ATQFSMAHQD VRYYLNGMLF ETEGEELRTV ATDGHRLAVC 

       190        200        210        220        230        240 
SMPIGQSLPS HSVIVPRKGV IELMRMLDGG DNPLRVQIGS NNIRAHVGDF IFTSKLVDGR 

       250        260        270        280        290        300 
FPDYRRVLPK NPDKHLEAGC DLLKQAFARA AILSNEKFRG VRLYVSENQL KITANNPEQE 

       310        320        330        340        350        360 
EAEEILDVTY SGAEMEIGFN VSYVLDVLNA LKCENVRMML TDSVSSVQIE DAASQSAAYV 


VMPMRL

« Hide

Hide | Top

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structural analysis of the dnaA and dnaN genes of Escherichia coli." Ohmori H., Kimura M., Nagata T., Sakakibara Y. Gene 28:159-170(1984) [PubMed: 6234204] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed: 7686882] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"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.
[5]	"Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12." Armengod M.E.E., Garcca-Sogo M., Lambies E. J. Biol. Chem. 263:12109-12114(1988) [PubMed: 2841344] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-14.
[6]	"Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences." Armengod M.E.E., Lambies E. Gene 43:183-196(1986) [PubMed: 3527871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 143-170.
[7]	"Molecular analysis of the recF gene of Escherichia coli." Blanar M.A., Sandler S.J., Armengod M.-E., Ream L.W., Clark A.J. Proc. Natl. Acad. Sci. U.S.A. 81:4622-4626(1984) [PubMed: 6379647] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 297-366.
[8]	"DNA sequence and transcription of the region upstream of the E. coli gyrB gene." Adachi T., Mizuuchi K., Menzel R., Gellert M. Nucleic Acids Res. 12:6389-6395(1984) [PubMed: 6089112] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 342-366.
[9]	"Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp." Kong X.-P., Onrust R., O'Donnell M., Kuriyan J. Cell 69:425-437(1992) [PubMed: 1349852] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[10]	"Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III." Oakley A.J., Prosselkov P., Wijffels G., Beck J.L., Wilce M.C., Dixon N.E. Acta Crystallogr. D 59:1192-1199(2003) [PubMed: 12832762] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
[11]	"Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp." Bunting K.A., Roe S.M., Pearl L.H. EMBO J. 22:5883-5892(2003) [PubMed: 14592985] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH DINB.
[12]	"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.
+	Additional computationally mapped references.

Hide | Top

Cross-references

Sequence databases

J01602 Genomic DNA. Translation: AAB59150.1.
L10328 Genomic DNA. Translation: AAA62052.1.
U00096 Genomic DNA. Translation: AAC76724.1.
AP009048 Genomic DNA. Translation: BAE77593.1.
M19876 Genomic DNA. Translation: AAA23695.1.
M13822 Genomic DNA. Translation: AAA24512.1.
K02179 Genomic DNA. Translation: AAA24510.1.
X04341 Genomic DNA. Translation: CAA27869.1.

PIR

DJEC3B. A91510.

RefSeq

AP_004092.1.
NP_418156.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JQJ	X-ray	2.90	A/B	1-366	[»]
1JQL	X-ray	2.50	A	1-366	[»]
1MMI	X-ray	1.85	A/B	1-366	[»]
1OK7	X-ray	1.65	A/B	1-366	[»]
1UNN	X-ray	1.90	A/B	1-366	[»]
1WAI	model	-	A/B	1-366	[»]
2POL	X-ray	2.50	A/B	1-366	[»]
3BEP	X-ray	1.92	A/B	1-366	[»]
3D1E	X-ray	1.90	A/B	1-366	[»]
3D1F	X-ray	2.00	A/B	1-366	[»]
3D1G	X-ray	1.64	A/B	1-366	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A988. 28 interactions.

2-D gel databases

ECO2DBASE

A036.1. 6TH EDITION.
B036.1. 6TH EDITION.

Genome annotation databases

GeneID

948218.

GenomeReviews

Gene locus JW3678 in contig AP009048_GR.
Gene locus b3701 in contig U00096_GR.

KEGG

ecj:JW3678.
eco:b3701.

Organism-specific databases

EchoBASE

EB0238.

EcoGene

EG10242. dnaN.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A988.

OMA

P0A988. IGFNARY.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10242-MON.

Family and domain databases

InterPro

IPR001001. DNA_polIII_beta.
[Graphical view]

Gene3D

G3DSA:3.10.150.10. DNA_polIII_beta. 3 hits.

Pfam

PF00712. DNA_pol3_beta. 1 hit.
PF02767. DNA_pol3_beta_2. 1 hit.
PF02768. DNA_pol3_beta_3. 1 hit.
[Graphical view]

SMART

SM00480. POL3Bc. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00663. dnan. 1 hit.

ProtoNet

Search...

Hide | Top

Entry information

Entry name

DPO3B_ECOLI

Accession

Primary (citable) accession number: P0A988
Secondary accession number(s): P00583, Q2M813

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	April 1, 1988
Last modified:	June 16, 2009
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

Hide | Top

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 and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2-D gel databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents