Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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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 holoenzyme responsible for most of the replicative synthesis in bacteria [ (PUBMED:8548826) ]. It functions by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing DNA chain, using a complementary DNA as template. The elongation factor beta-clamp, also called beta subunit, is part of the DNA polymerase III holoenzyme. However, beta-clamp is not attached to polymerase III permanently like the other subunits. It is loaded on the DNA, by clamp loader, a subunit of DNA Pol III [ (PUBMED:27499105) ]. The beta clamp forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The bacterial beta clamp is a homodimer; each monomer consists of three globular domains to yield a six-domain ring [ (PUBMED:18191219) ]. It is structurally similar to the trimeric ring formed by proliferating cell nuclear antigen (PCNA) (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69) [ (PUBMED:1358275) ]. This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
GO process:	DNA replication (GO:0006260)
GO component:	DNA polymerase III complex (GO:0009360)
GO function:	DNA binding (GO:0003677)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 21350 POL3Bc domains in 21350 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing POL3Bc domain.

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

  Click on the protein counts, or double click on taxonomic names to display all proteins containing POL3Bc domain in the selected taxonomic class.

• 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
  2xur		The G157C mutation in the Escherichia coli sliding clamp specifically affects initiation of replication
  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
  3p16		Crystal structure of DNA polymerase III sliding clamp
  3pwe		Crystal structure of the E. coli beta clamp mutant R103C, I305C, C260S, C333S at 2.2A resolution
  3q4j		Structure of a small peptide ligand bound to E.coli DNA sliding clamp
  3q4k		Structure of a small peptide ligand bound to E.coli DNA sliding clamp
  3q4l		Structure of a small peptide ligand bound to E.coli DNA sliding clamp
  3qsb		Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile
  3rb9		Crystal structure of the M. tuberculosis beta clamp
  3t0p		Crystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from Eubacterium rectale ATCC 33656 at 2.26 A resolution
  4k3k		E. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)-3-phenylpropanoic acid
  4k3l		E. coli sliding clamp in complex with AcLF dipeptide
  4k3m		E.coli sliding clamp in complex with AcALDLF peptide
  4k3o		E. coli sliding clamp in complex with AcQADLF
  4k3p		E. coli sliding clamp in complex with AcQLALF
  4k3q		E. coli sliding clamp in complex with AcQLDAF
  4k3r		E. coli sliding clamp in complex with AcQLDLA
  4k3s		E. coli sliding clamp in P1 crystal space group
  4k74		The UmuC subunit of the E. coli DNA polymerase V shows a unique interaction with the beta-clamp processivity factor.
  4mjp		E. coli sliding clamp in complex with (R)-Vedaprofen
  4mjq		E. coli sliding clamp in complex with Bromfenac
  4mjr		E. coli sliding clamp in complex with (S)-Carprofen
  4n94		E. coli sliding clamp in complex with 3,4-difluorobenzamide
  4n95		E. coli sliding clamp in complex with 5-chloroindoline-2,3-dione
  4n96		E. coli sliding clamp in complex with 6-nitroindazole
  4n97		E. coli sliding clamp in complex with 5-nitroindole
  4n98		E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid
  4n99		E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid
  4n9a		E. coli sliding clamp in complex with (R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxylic acid
  4ovf		E. coli sliding clamp in complex with (R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
  4ovg		E. coli sliding clamp in complex with (R)-9-(2-amino-2-oxoethyl)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
  4ovh		E. coli sliding clamp in complex with (R)-6-bromo-9-(2-(carboxymethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
  4pnu		E. coli sliding clamp in complex with (R)-6-bromo-9-(2-((R)-1-carboxy-2-phenylethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
  4pnv		E. coli sliding clamp apo-crystal in P21 space group with larger cell dimensions
  4pnw		E. coli sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-carboxy-2-phenylethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
  4rki		4RKI
  4s3i		4S3I
  4tr6		4TR6
  4tr7		4TR7
  4tr8		4TR8
  4trt		4TRT
  4tsz		4TSZ
  5agu		5AGU
  5agv		5AGV
  5ah2		5AH2
  5ah4		5AH4
  5fku		5FKU
  5fkv		5FKV
  5fkw		5FKW
  5frq		5FRQ

• Links (links to other resources describing this domain)

• INTERPRO	IPR001001
  PFAM	DNA_pol3_beta

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