DNA polymerase III subunit beta

Details

Name
DNA polymerase III subunit beta
Kind
protein
Synonyms
  • 2.7.7.7
  • Beta clamp
  • Beta sliding clamp
Gene Name
dnaN
UniProtKB Entry
P0A988Swiss-Prot
Organism
Escherichia coli (strain K12)
NCBI Taxonomy ID
83333
Amino acid sequence
>lcl|BSEQ0017219|DNA polymerase III subunit beta
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL
Number of residues
366
Molecular Weight
40586.255
Theoretical pI
5.05
GO Classification
Functions
3'-5' exonuclease activity / DNA binding / DNA-directed DNA polymerase activity / identical protein binding
Processes
cellular response to DNA damage stimulus / DNA strand elongation involved in DNA replication
Components
cytosol / DNA polymerase III complex
General Function
Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA (PubMed:2040637). DNA bound in the ring is bent 22 degrees, in solution primed DNA is bound more tightly than dsDNA, suggesting the clamp binds both ss- and dsDNA (PubMed:18191219). In a complex of DNA with this protein, alpha, epsilon and tau subunits however the DNA is only slightly bent (PubMed:26499492). Coordinates protein traffic at the replication fork, where it interacts with multiple DNA polymerases, repair factors and other proteins (PubMed:14592985, PubMed:14729336, PubMed:15466025, PubMed:15952889, PubMed:16168375, PubMed:22716942, PubMed:26499492). Initially characterized for its ability to contact the alpha subunit (dnaE) of DNA polymerase III (Pol III), tethering it to the DNA and conferring very high processivity (PubMed:2040637). Pol III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; it also exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication (PubMed:2040637, PubMed:3519609). A single clamp can bind both Pol III and IV, allowing the repair Pol IV to access DNA when it is damaged and needs to be fixed, a process the replicative polymerase cannot perform; when DNA is repaired Pol III takes over again (PubMed:16168375). Serves as a processivity factor for DNA polymerases II (PubMed:1999435, PubMed:1534562), IV (PubMed:10801133) and V (PubMed:10801133). A shorter protein beta* may be important for increasing survival after UV irradiation, and stimulates DNA synthesis with increased processivity in the presence of core Pol III plus the clamp loader complex (PubMed:8576210, PubMed:8576212).
Specific Function
3'-5' exonuclease activity
Pfam Domain Function
Signal Regions
Not Available
Transmembrane Regions
Not Available
Cellular Location
Cytoplasm
Gene sequence
>lcl|BSEQ0017220|DNA polymerase III subunit beta (dnaN)
ATGAAATTTACCGTAGAACGTGAGCATTTATTAAAACCGCTACAACAGGTGAGCGGTCCG
TTAGGTGGTCGTCCTACGCTACCGATTCTCGGTAATCTGCTGTTACAGGTTGCTGACGGT
ACGTTGTCGCTGACCGGTACTGATCTCGAGATGGAAATGGTGGCACGTGTTGCGCTGGTT
CAGCCACACGAGCCAGGAGCGACGACCGTTCCGGCGCGCAAATTCTTTGATATCTGCCGT
GGTCTGCCTGAAGGCGCGGAAATTGCCGTGCAGCTGGAAGGTGAACGGATGCTGGTACGC
TCCGGGCGTAGCCGTTTTTCGCTGTCTACCCTGCCAGCGGCGGATTTCCCGAACCTCGAT
GACTGGCAGAGTGAAGTCGAATTTACCCTGCCGCAGGCAACGATGAAGCGTCTGATTGAA
GCGACCCAGTTTTCTATGGCGCATCAGGACGTTCGCTATTACTTAAATGGTATGCTGTTT
GAAACCGAAGGTGAAGAACTGCGCACCGTGGCAACCGACGGCCACCGTCTGGCGGTCTGT
TCAATGCCAATTGGTCAATCTTTGCCAAGCCATTCGGTGATCGTACCGCGTAAAGGCGTG
ATTGAACTGATGCGTATGCTCGACGGCGGCGACAATCCGCTGCGCGTACAGATTGGCAGC
AACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGC
TTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATCTGGAAGCTGGCTGC
GATCTGCTCAAGCAGGCGTTTGCTCGCGCGGCGATTCTCTCTAACGAGAAATTCCGCGGC
GTACGTCTTTATGTCAGCGAAAACCAGCTGAAAATCACCGCCAACAACCCGGAACAGGAA
GAAGCGGAAGAGATCCTCGACGTTACCTATAGCGGTGCGGAGATGGAAATCGGCTTCAAC
GTCAGTTATGTGCTGGATGTTCTGAACGCGCTGAAATGCGAAAACGTCCGCATGATGCTG
ACCGATTCGGTTTCCAGCGTGCAGATTGAAGATGCGGCCAGCCAGAGCGCGGCTTATGTT
GTCATGCCAATGAGACTGTAA
Chromosome Location
Not Available
Locus
Not Available
External Identifiers
ResourceLink
UniProtKB IDP0A988
UniProtKB Entry NameDPO3B_ECOLI
GenBank Protein ID145759
GenBank Gene IDJ01602
PDB ID(s)1JQJ, 1JQL, 1MMI, 1OK7, 1UNN, 1WAI, 2POL, 2XUR, 3BEP, 3D1E, 3D1F, 3D1G, 3F1V, 3PWE, 3Q4J, 3Q4K, 3Q4L, 3QSB, 4K3K, 4K3L, 4K3M, 4K3O, 4K3P, 4K3Q, 4K3R, 4K3S, 4MJP, 4MJQ, 4MJR, 4N94, 4N95, 4N96, 4N97, 4N98, 4N99, 4N9A
KEGG IDecj:JW3678
NCBI Gene ID948218
General References
  1. Ohmori H, Kimura M, Nagata T, Sakakibara Y: Structural analysis of the dnaA and dnaN genes of Escherichia coli. Gene. 1984 May;28(2):159-70. [Article]
  2. Burland V, Plunkett G 3rd, Daniels DL, Blattner FR: DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics. 1993 Jun;16(3):551-61. [Article]
  3. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. [Article]
  4. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21. [Article]
  5. Armengod ME, Garcia-Sogo M, Lambies E: Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12. J Biol Chem. 1988 Aug 25;263(24):12109-14. [Article]
  6. Armengod ME, Lambies E: Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences. Gene. 1986;43(3):183-96. [Article]
  7. Blanar MA, Sandler SJ, Armengod ME, Ream LW, Clark AJ: Molecular analysis of the recF gene of Escherichia coli. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4622-6. [Article]
  8. Adachi T, Mizuuchi K, Menzel R, Gellert M: DNA sequence and transcription of the region upstream of the E. coli gyrB gene. Nucleic Acids Res. 1984 Aug 24;12(16):6389-95. [Article]
  9. VanBogelen RA, Abshire KZ, Moldover B, Olson ER, Neidhardt FC: Escherichia coli proteome analysis using the gene-protein database. Electrophoresis. 1997 Aug;18(8):1243-51. [Article]
  10. Kurz M, Dalrymple B, Wijffels G, Kongsuwan K: Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein. J Bacteriol. 2004 Jun;186(11):3508-15. [Article]
  11. Sutton MD: The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction. J Bacteriol. 2004 Oct;186(20):6738-48. [Article]
  12. Su'etsugu M, Nakamura K, Keyamura K, Kudo Y, Katayama T: Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis. J Biol Chem. 2008 Dec 26;283(52):36118-31. doi: 10.1074/jbc.M803158200. Epub 2008 Oct 30. [Article]
  13. Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC: Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell. 2009 Dec 11;36(5):845-60. doi: 10.1016/j.molcel.2009.11.024. [Article]
  14. Baxter JC, Sutton MD: Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA. Mol Microbiol. 2012 Aug;85(4):648-68. doi: 10.1111/j.1365-2958.2012.08129.x. Epub 2012 Jul 13. [Article]
  15. Ozaki S, Matsuda Y, Keyamura K, Kawakami H, Noguchi Y, Kasho K, Nagata K, Masuda T, Sakiyama Y, Katayama T: A replicase clamp-binding dynamin-like protein promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in E. coli. Cell Rep. 2013 Sep 12;4(5):985-95. doi: 10.1016/j.celrep.2013.07.040. Epub 2013 Aug 30. [Article]
  16. 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 May 1;69(3):425-37. [Article]
  17. Oakley AJ, Prosselkov P, Wijffels G, Beck JL, Wilce MC, Dixon NE: Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III. Acta Crystallogr D Biol Crystallogr. 2003 Jul;59(Pt 7):1192-9. Epub 2003 Jun 27. [Article]
  18. Bunting KA, Roe SM, Pearl LH: Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J. 2003 Nov 3;22(21):5883-92. [Article]
  19. O'Donnell M: Accessory protein function in the DNA polymerase III holoenzyme from E. coli. Bioessays. 1992 Feb;14(2):105-11. [Article]

Associated Data

Drug Relations
DrugDrug groupPharmacological action?TypeActionsDetails
[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acidexperimentalunknowntargetDetails