Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P0A988 (DPO3B_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length366 AA.
Sequence statusComplete.
Protein existenceEvidence 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. Binds to CrfC homooligomers at the midcell position during DNA replication. Ref.10 Ref.11 Ref.12 Ref.14

Subcellular location

Cytoplasm. Note: Localizes to midcell position when chromosomes are condensed during DNA replication. Ref.14

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 366366DNA polymerase III subunit beta
PRO_0000105434

Regions

Region1 – 125125I
Region126 – 253128II
Region254 – 366113III

Experimental info

Mutagenesis661G → 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
Mutagenesis1741G → 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

......................................................................... 366
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A988 [UniParc].

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

FASTA36640,587
        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

References

« Hide '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 277:1453-1462(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]"A replicase clamp-binding dynamin-like protein promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in E. coli."
Ozaki S., Matsuda Y., Keyamura K., Kawakami H., Noguchi Y., Kasho K., Nagata K., Masuda T., Sakiyama Y., Katayama T.
Cell Rep. 4:985-995(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CRFC, SUBUNIT, SUBCELLULAR LOCATION.
Strain: K12 / MG1655 / ATCC 47076.
[15]"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).
[16]"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).
[17]"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.
[18]"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.
PIRDJEC3B. A91510.
RefSeqNP_418156.1. NC_000913.3.
YP_491734.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90A/B1-366[»]
1JQLX-ray2.50A1-366[»]
1MMIX-ray1.85A/B1-366[»]
1OK7X-ray1.65A/B1-366[»]
1UNNX-ray1.90A/B1-366[»]
1WAImodel-A/B1-366[»]
2POLX-ray2.50A/B1-366[»]
2XURX-ray1.90A/B1-366[»]
3BEPX-ray1.92A/B1-366[»]
3D1EX-ray1.90A/B1-366[»]
3D1FX-ray2.00A/B1-366[»]
3D1GX-ray1.64A/B1-366[»]
3F1VX-ray1.77A/B1-366[»]
3PWEX-ray2.20A/B1-366[»]
3Q4JX-ray2.30A/B/C/D/E/F1-366[»]
3Q4KX-ray2.60A/B1-366[»]
3Q4LX-ray1.95A/B1-366[»]
3QSBX-ray1.90A/B1-366[»]
4K3KX-ray1.85A/B1-366[»]
4K3LX-ray1.50A/B1-366[»]
4K3MX-ray1.85A/B1-366[»]
4K3OX-ray2.00A/B1-366[»]
4K3PX-ray2.15A/B1-366[»]
4K3QX-ray1.85A/B1-366[»]
4K3RX-ray1.86A/B1-366[»]
4K3SX-ray1.75A/B1-366[»]
4MJPX-ray1.86A/B1-366[»]
4MJQX-ray1.73A/B1-366[»]
4MJRX-ray1.62A/B1-366[»]
4N94X-ray1.73A/B1-366[»]
4N95X-ray1.80A/B1-366[»]
4N96X-ray1.70A/B1-366[»]
4N97X-ray1.97A/B1-366[»]
4N98X-ray1.70A/B1-366[»]
4N99X-ray2.30A/B1-366[»]
4N9AX-ray1.90A/B1-366[»]
ProteinModelPortalP0A988.
SMRP0A988. Positions 1-366.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36038N.
IntActP0A988. 38 interactions.
STRING511145.b3701.

Proteomic databases

PaxDbP0A988.
PRIDEP0A988.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76724; AAC76724; b3701.
BAE77593; BAE77593; BAE77593.
GeneID12930541.
948218.
KEGGecj:Y75_p3472.
eco:b3701.
PATRIC32122899. VBIEscCol129921_3825.

Organism-specific databases

EchoBASEEB0238.
EcoGeneEG10242. dnaN.

Phylogenomic databases

eggNOGCOG0592.
HOGENOMHOG000071791.
KOK02338.
OMAAVCSMPV.
OrthoDBEOG65J53F.
PhylomeDBP0A988.

Enzyme and pathway databases

BioCycEcoCyc:EG10242-MONOMER.
ECOL316407:JW3678-MONOMER.

Gene expression databases

GenevestigatorP0A988.

Family and domain databases

InterProIPR001001. DNA_polIII_beta.
IPR022635. DNA_polIII_beta_C.
IPR022637. DNA_polIII_beta_cen.
IPR022634. DNA_polIII_beta_N.
[Graphical view]
PfamPF00712. DNA_pol3_beta. 1 hit.
PF02767. DNA_pol3_beta_2. 1 hit.
PF02768. DNA_pol3_beta_3. 1 hit.
[Graphical view]
PIRSFPIRSF000804. DNA_pol_III_b. 1 hit.
SMARTSM00480. POL3Bc. 1 hit.
[Graphical view]
TIGRFAMsTIGR00663. dnan. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0A988.
PROP0A988.

Entry information

Entry nameDPO3B_ECOLI
AccessionPrimary (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 11, 2014
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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