P0A988 (DPO3B_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA polymerase III subunit beta
EC=2.7.7.7

Alternative name(s):
Beta sliding clamp
Short name=Beta clamp

Gene names

Name:	dnaN
Ordered Locus Names:	b3701, JW3678

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	366 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 beta chain is required for initiation of replication; once it is clamped onto DNA it slides freely (bidirectional and ATP-independent) along duplex DNA. Coordinates protein traffic at the replication fork, where it interacts with multiple DNA polymerases. Ref.11 Ref.13
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 beta sliding clamp processivity factor (this entry). 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. Can also be part of the RIDA complex (regulatory inactivation of DnaA), consisting of ATP-DnaA, ADP-Hda and DNA-loaded beta clamp. Probably also interacts with components of DNA polymerases I, II, IV and V. Ref.10 Ref.11 Ref.12
Subcellular location	Cytoplasm.
Miscellaneous	The temperature- and UV-sensitive allele dnaN159 does not grow at higher than 37 degrees Celsius. The global SOS response is chronically induced. The UV-sensitivity of dnaN159 is dependent upon pol IV (dinB), it has an enhanced Pol V-dependent mutation rate (umuC, umuD), and is absolutely dependent on the polymerase activity of Pol I (polA) for viability.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Cytoplasm
Molecular function	DNA-directed DNA polymerase Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA strand elongation involved in DNA replication Inferred from direct assay PubMed 3519609. Source: EcoCyc response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki
Cellular_component	DNA polymerase III complex Inferred from electronic annotation. Source: InterPro cytosol Inferred from direct assay PubMed 16858726. 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
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		3	EBI-542385,EBI-542385
dnaE	P10443	3	EBI-542385,EBI-549111
dnaX	P06710	4	EBI-542385,EBI-549140
hda	P69931	3	EBI-542385,EBI-545453
holA	P28630	9	EBI-542385,EBI-549153
rpe	P0AG07	2	EBI-542385,EBI-546020
tnsE	P05845	4	EBI-542385,EBI-2434514	From a different organism.

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

I

Region

126 – 253

128

II

Region

254 – 366

113

III

Experimental info

Mutagenesis

66

1

G → E in dnaN159; a temperature- and UV-sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-174. Ref.11

Mutagenesis

174

1

G → A in dnaN159; a temperature- and UV-sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-66. Ref.11

Secondary structure

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366

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Helix

7 – 17

11

Turn

18 – 20

3

Helix

28 – 31

4

Beta strand

32 – 38

7

Beta strand

41 – 47

7

Beta strand

49 – 58

10

Beta strand

66 – 71

6

Helix

72 – 81

10

Beta strand

87 – 93

7

Beta strand

96 – 101

6

Beta strand

104 – 109

6

Helix

113 – 115

3

Beta strand

125 – 130

6

Helix

132 – 142

11

Helix

143 – 145

3

Helix

153 – 155

3

Beta strand

156 – 172

17

Beta strand

174 – 196

23

Helix

197 – 205

9

Beta strand

209 – 211

3

Beta strand

214 – 218

5

Beta strand

220 – 227

8

Beta strand

230 – 235

6

Helix

244 – 247

4

Beta strand

254 – 259

6

Helix

260 – 272

13

Turn

276 – 278

3

Beta strand

280 – 286

7

Beta strand

289 – 295

7

Beta strand

301 – 307

7

Beta strand

309 – 313

5

Beta strand

315 – 320

6

Helix

321 – 330

10

Beta strand

333 – 340

8

Beta strand

343 – 345

3

Beta strand

347 – 351

5

Beta strand

354 – 361

8

Sequences

	Sequence		Length	Mass (Da)
	P0A988 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 7A45646F61255B5A	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

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 342-366.
[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]	"Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein." Kurz M., Dalrymple B., Wijffels G., Kongsuwan K. J. Bacteriol. 186:3508-3515(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HDA.
[11]	"The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction." Sutton M.D. J. Bacteriol. 186:6738-6748(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AT REPLICATION FORK, INTERACTION WITH DNAE, MUTAGENESIS OF GLY-66 AND GLY-174.
[12]	"Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis." Su'etsugu M., Nakamura K., Keyamura K., Kudo Y., Katayama T. J. Biol. Chem. 283:36118-36131(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN RIDA COMPLEX.
[13]	"Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA." Baxter J.C., Sutton M.D. Mol. Microbiol. 85:648-668(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN REPLICATION FORK.
[14]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[15]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
[16]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH DINB.
[17]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

NP_418156.1. NC_000913.2.
YP_491734.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
2XUR	X-ray	1.90	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	[»]
3F1V	X-ray	1.77	A/B	1-366	[»]
3PWE	X-ray	2.20	A/B	1-366	[»]
3Q4J	X-ray	2.30	A/B/C/D/E/F	1-366	[»]
3Q4K	X-ray	2.60	A/B	1-366	[»]
3Q4L	X-ray	1.95	A/B	1-366	[»]
3QSB	X-ray	1.90	A/B	1-366	[»]

ProteinModelPortal

P0A988.

SMR

P0A988. Positions 1-366.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36038N.

IntAct

P0A988. 35 interactions.

STRING

511145.b3701.

Proteomic databases

PaxDb

P0A988.

PRIDE

P0A988.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76724; AAC76724; b3701.
BAE77593; BAE77593; BAE77593.

GeneID

12930541.
948218.

KEGG

ecj:Y75_p3472.
eco:b3701.

PATRIC

32122899. VBIEscCol129921_3825.

Organism-specific databases

EchoBASE

EB0238.

EcoGene

EG10242. dnaN.

Phylogenomic databases

eggNOG

COG0592.

HOGENOM

HOG000071791.

KO

K02338.

OMA

DYNRVIP.

ProtClustDB

PRK05643.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10242-MONOMER.
ECOL316407:JW3678-MONOMER.

Gene expression databases

Genevestigator

P0A988.

Family and domain databases

InterPro

IPR001001. DNA_polIII_beta.
IPR022635. DNA_polIII_beta_C.
IPR022637. DNA_polIII_beta_cen.
IPR022634. DNA_polIII_beta_N.
[Graphical view]

Pfam

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

PIRSF

PIRSF000804. DNA_pol_III_b. 1 hit.

SMART

SM00480. POL3Bc. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00663. dnan. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A988.

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:	May 29, 2013
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program