Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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POL3Bc DNA polymerase III beta subunit

SMART accession number:	SM00480
Description:
Interpro abstract (IPR001001):	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.
GO process:	DNA replication (GO:0006260)
GO component:	DNA polymerase III complex (GO:0009360)
GO function:	3'-5' exonuclease activity (GO:0008408), DNA-directed DNA polymerase activity (GO:0003887), DNA binding (GO:0003677)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 1797 POL3Bc domains in 1797 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a POL3Bc domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with POL3Bc domain is also avaliable.

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• Cellular role (predicted cellular role)

• Cellular role: replication
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Kong XP, Onrust R, O'Donnell M, Kuriyan J
  • Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp.
  • Cell. 1992; 69: 425-37
  • Display abstract

  • The crystal structure of the beta subunit (processivity factor) of DNA polymerase III holoenzyme has been determined at 2.5 A resolution. A dimer of the beta subunit (M(r) = 2 x 40.6 kd, 2 x 366 amino acid residues) forms a ring-shaped structure lined by 12 alpha helices that can encircle duplex DNA. The structure is highly symmetrical, with each monomer containing three domains of identical topology. The charge distribution and orientation of the helices indicate that the molecule functions by forming a tight clamp that can slide on DNA, as shown biochemically. A potential structural relationship is suggested between the beta subunit and proliferating cell nuclear antigen (PCNA, the eukaryotic polymerase delta [and epsilon] processivity factor), and the gene 45 protein of the bacteriophage T4 DNA polymerase.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 100.00 map03030 DNA replication This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with POL3Bc domain which could be assigned to a KEGG orthologous group, and not all proteins containing POL3Bc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of POL3Bc domains in PDB

  PDB code	Main view	Title
  1jqj		Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of e. coli dna polymerase iii: structure of the beta-delta complex
  1jql		Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of e. coli dna polymerase iii: structure of beta-delta (1-140)
  1mmi		E. coli dna polymerase beta subunit
  1ok7		A conserved protein binding-site on bacterial sliding clamps
  1unn		Complex of beta-clamp processivity factor and little finger domain of poliv
  1vpk		Crystal structure of dna polymerase iii, beta subunit (tm0262) from thermotoga maritima at 2.00 a resolution
  2avt		Crystal structure of the beta subunit from dna polymerase of streptococcus pyogenes
  2awa		Crystal structure of dna polymerase iii, beta chain (ec 2.7.7.7) (np_344555.1) from streptococcus pneumoniae tigr4 at 2.50 a resolution
  2pol		Three-dimensional structure of the beta subunit of escherichia coli dna polymerase iii holoenzyme: a sliding dna clamp
  3bep		Structure of a sliding clamp on dna
  3d1e		Crystal structure of e. coli sliding clamp (beta) bound to a polymerase ii peptide
  3d1f		Crystal structure of e. coli sliding clamp (beta) bound to a polymerase iii peptide
  3d1g		Structure of a small molecule inhibitor bound to a dna sliding clamp
  3f1v		E. coli beta sliding clamp, 148-153 ala mutant

• Links (links to other resources describing this domain)

• PFAM	DNA_pol3_beta
  INTERPRO	IPR001001

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