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Beta sliding clamp (Beta clamp) (Sliding clamp) (Beta-clamp processivity factor) (DNA polymerase III beta sliding clamp subunit)

 DPO3B_ECOLI             Reviewed;         366 AA.
P0A988; P00583; Q2M813;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
01-APR-1988, sequence version 1.
07-NOV-2018, entry version 122.
RecName: Full=Beta sliding clamp {ECO:0000303|PubMed:2040637};
Short=Beta clamp;
Short=Sliding clamp;
AltName: Full=Beta-clamp processivity factor;
AltName: Full=DNA polymerase III beta sliding clamp subunit;
Name=dnaN; OrderedLocusNames=b3701, JW3678;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6234204; DOI=10.1016/0378-1119(84)90253-1;
Ohmori H., Kimura M., Nagata T., Sakakibara Y.;
"Structural analysis of the dnaA and dnaN genes of Escherichia coli.";
Gene 28:159-170(1984).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7686882; DOI=10.1006/geno.1993.1230;
Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
"DNA sequence and analysis of 136 kilobases of the Escherichia coli
genome: organizational symmetry around the origin of replication.";
Genomics 16:551-561(1993).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-14.
PubMed=2841344;
Armengod M.E.E., Garcca-Sogo M., Lambies E.;
"Transcriptional organization of the dnaN and recF genes of
Escherichia coli K-12.";
J. Biol. Chem. 263:12109-12114(1988).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 143-170.
PubMed=3527871; DOI=10.1016/0378-1119(86)90206-4;
Armengod M.E.E., Lambies E.;
"Overlapping arrangement of the recF and dnaN operons of Escherichia
coli; positive and negative control sequences.";
Gene 43:183-196(1986).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 297-366.
PubMed=6379647; DOI=10.1073/pnas.81.15.4622;
Blanar M.A., Sandler S.J., Armengod M.-E., Ream L.W., Clark A.J.;
"Molecular analysis of the recF gene of Escherichia coli.";
Proc. Natl. Acad. Sci. U.S.A. 81:4622-4626(1984).
[8]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 342-366.
PubMed=6089112; DOI=10.1093/nar/12.16.6389;
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. 12:6389-6395(1984).
[9]
FUNCTION AS PROCESSIVITY FACTOR.
PubMed=3519609;
LaDuca R.J., Crute J.J., McHenry C.S., Bambara R.A.;
"The beta subunit of the Escherichia coli DNA polymerase III
holoenzyme interacts functionally with the catalytic core in the
absence of other subunits.";
J. Biol. Chem. 261:7550-7557(1986).
[10]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[11]
FUNCTION WITH DNA POLYMERASE II (POLB), AND SUBUNIT.
PubMed=1999435;
Hughes A.J. Jr., Bryan S.K., Chen H., Moses R.E., McHenry C.S.;
"Escherichia coli DNA polymerase II is stimulated by DNA polymerase
III holoenzyme auxiliary subunits.";
J. Biol. Chem. 266:4568-4573(1991).
[12]
FUNCTION AS A TETHER, SUBUNIT, AND INTERACTION WITH DNAE.
PubMed=2040637;
Stukenberg P.T., Studwell-Vaughan P.S., O'Donnell M.;
"Mechanism of the sliding beta-clamp of DNA polymerase III
holoenzyme.";
J. Biol. Chem. 266:11328-11334(1991).
[13]
FUNCTION WITH DNA POLYMERASE II (POLB), AND SUBUNIT.
PubMed=1534562;
Bonner C.A., Stukenberg P.T., Rajagopalan M., Eritja R., O'Donnell M.,
McEntee K., Echols H., Goodman M.F.;
"Processive DNA synthesis by DNA polymerase II mediated by DNA
polymerase III accessory proteins.";
J. Biol. Chem. 267:11431-11438(1992).
[14]
IDENTIFICATION OF ISOFORM BETA*, FUNCTION, AND INDUCTION BY UV.
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=8576210; DOI=10.1074/jbc.271.5.2478;
Skaliter R., Paz-Elizur T., Livneh Z.;
"A smaller form of the sliding clamp subunit of DNA polymerase III is
induced by UV irradiation in Escherichia coli.";
J. Biol. Chem. 271:2478-2481(1996).
[15]
ALTERNATIVE PROMOTER USAGE (ISOFORMS BETA AND BETA*), INDUCTION BY
NALIDIXIC ACID, AND MUTAGENESIS OF ALA-133; MET-135 AND MET-146.
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=8576211; DOI=10.1074/jbc.271.5.2482;
Paz-Elizur T., Skaliter R., Blumenstein S., Livneh Z.;
"Beta*, a UV-inducible smaller form of the beta subunit sliding clamp
of DNA polymerase III of Escherichia coli. I. Gene expression and
regulation.";
J. Biol. Chem. 271:2482-2490(1996).
[16]
CHARACTERIZATION OF BETA*, AND SUBUNIT.
PubMed=8576212; DOI=10.1074/jbc.271.5.2491;
Skaliter R., Bergstein M., Livneh Z.;
"Beta*, a UV-inducible shorter form of the beta subunit of DNA
polymerase III of Escherichia coli. II. Overproduction, purification,
and activity as a polymerase processivity clamp.";
J. Biol. Chem. 271:2491-2496(1996).
[17]
RING OPENING BY DELTA SUBUNIT (HOLA), AND SUBUNIT.
PubMed=9927437; DOI=10.1093/emboj/18.3.771;
Turner J., Hingorani M.M., Kelman Z., O'Donnell M.;
"The internal workings of a DNA polymerase clamp-loading machine.";
EMBO J. 18:771-783(1999).
[18]
FUNCTION WITH DNA POLYMERASES IV (DINB) AND V (UMUCD).
PubMed=10801133; DOI=10.1038/35010020;
Tang M., Pham P., Shen X., Taylor J.S., O'Donnell M., Woodgate R.,
Goodman M.F.;
"Roles of E. coli DNA polymerases IV and V in lesion-targeted and
untargeted SOS mutagenesis.";
Nature 404:1014-1018(2000).
[19]
INTERACTION WITH MUTS; LIGASE AND POLA.
PubMed=11459978; DOI=10.1073/pnas.121009498;
Lopez de Saro F.J., O'Donnell M.;
"Interaction of the beta sliding clamp with MutS, ligase, and DNA
polymerase I.";
Proc. Natl. Acad. Sci. U.S.A. 98:8376-8380(2001).
[20]
INTERACTION WITH DINB; DNAE; HOLA; MUTS; POLB AND UMUC.
STRAIN=K12 / XL1-Blue;
PubMed=11573000; DOI=10.1073/pnas.191384398;
Dalrymple B.P., Kongsuwan K., Wijffels G., Dixon N.E., Jennings P.A.;
"A universal protein-protein interaction motif in the eubacterial DNA
replication and repair systems.";
Proc. Natl. Acad. Sci. U.S.A. 98:11627-11632(2001).
[21]
CONSENSUS SEQUENCE FOR BINDING TO THE SLIDING CLAMP.
PubMed=15134440; DOI=10.1021/bi036229j;
Wijffels G., Dalrymple B.P., Prosselkov P., Kongsuwan K., Epa V.C.,
Lilley P.E., Jergic S., Buchardt J., Brown S.E., Alewood P.F.,
Jennings P.A., Dixon N.E.;
"Inhibition of protein interactions with the beta(2) sliding clamp of
Escherichia coli DNA polymerase III by peptides from beta(2)-binding
proteins.";
Biochemistry 43:5661-5671(2004).
[22]
INTERACTION WITH HDA.
PubMed=15150238; DOI=10.1128/JB.186.11.3508-3515.2004;
Kurz M., Dalrymple B., Wijffels G., Kongsuwan K.;
"Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related
protein.";
J. Bacteriol. 186:3508-3515(2004).
[23]
FUNCTION AT REPLICATION FORK, INTERACTION WITH DNAE, AND MUTAGENESIS
OF GLY-66 AND GLY-174.
PubMed=15466025; DOI=10.1128/JB.186.20.6738-6748.2004;
Sutton M.D.;
"The Escherichia coli dnaN159 mutant displays altered DNA polymerase
usage and chronic SOS induction.";
J. Bacteriol. 186:6738-6748(2004).
[24]
FUNCTION IN POLYMERASE CHOICE, SUBUNIT, AND MUTAGENESIS OF
272-ILE-LEU-273.
PubMed=16168375; DOI=10.1016/j.molcel.2005.08.011;
Indiani C., McInerney P., Georgescu R., Goodman M.F., O'Donnell M.;
"A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases
simultaneously.";
Mol. Cell 19:805-815(2005).
[25]
IDENTIFICATION IN RIDA COMPLEX.
PubMed=18977760; DOI=10.1074/jbc.M803158200;
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. 283:36118-36131(2008).
[26]
INDUCTION BY HYDROXYUREA.
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=20005847; DOI=10.1016/j.molcel.2009.11.024;
Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J.,
Walker G.C.;
"Hydroxyurea induces hydroxyl radical-mediated cell death in
Escherichia coli.";
Mol. Cell 36:845-860(2009).
[27]
REPLISOME COMPLEX, AND SUBUNIT.
PubMed=20413500; DOI=10.1126/science.1185757;
Reyes-Lamothe R., Sherratt D.J., Leake M.C.;
"Stoichiometry and architecture of active DNA replication machinery in
Escherichia coli.";
Science 328:498-501(2010).
[28]
REPLISOME COMPLEX, AND SUBUNIT.
PubMed=22157955; DOI=10.1038/nsmb.2179;
Georgescu R.E., Kurth I., O'Donnell M.E.;
"Single-molecule studies reveal the function of a third polymerase in
the replisome.";
Nat. Struct. Mol. Biol. 19:113-116(2011).
[29]
FUNCTION IN REPLICATION FORK, AND SUBUNIT.
PubMed=22716942; DOI=10.1111/j.1365-2958.2012.08129.x;
Baxter J.C., Sutton M.D.;
"Evidence for roles of the Escherichia coli Hda protein beyond
regulatory inactivation of DnaA.";
Mol. Microbiol. 85:648-668(2012).
[30]
INTERACTION WITH CRFC, SUBUNIT, AND SUBCELLULAR LOCATION.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=23994470; DOI=10.1016/j.celrep.2013.07.040;
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. 4:985-995(2013).
[31] {ECO:0000244|PDB:2POL}
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
PubMed=1349852; DOI=10.1016/0092-8674(92)90445-I;
Kong X.-P., 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 69:425-437(1992).
[32] {ECO:0000244|PDB:1JQJ, ECO:0000244|PDB:1JQL}
X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH DELTA SUBUNIT
(HOLA), PROBABLE MECHANISM OF CLAMP OPENING, AND MUTAGENESIS OF
272-ILE-LEU-273.
PubMed=11525728; DOI=10.1016/S0092-8674(01)00462-7;
Jeruzalmi D., Yurieva O., Zhao Y., Young M., Stewart J., Hingorani M.,
O'Donnell M., Kuriyan J.;
"Mechanism of processivity clamp opening by the delta subunit wrench
of the clamp loader complex of E. coli DNA polymerase III.";
Cell 106:417-428(2001).
[33] {ECO:0000244|PDB:1MMI}
X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
PubMed=12832762; DOI=10.1107/S0907444903009958;
Oakley A.J., Prosselkov P., Wijffels G., Beck J.L., Wilce M.C.,
Dixon N.E.;
"Flexibility revealed by the 1.85 A crystal structure of the beta
sliding-clamp subunit of Escherichia coli DNA polymerase III.";
Acta Crystallogr. D 59:1192-1199(2003).
[34] {ECO:0000244|PDB:1UNN}
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH DINB, AND
FUNCTION.
PubMed=14592985; DOI=10.1093/emboj/cdg568;
Bunting K.A., Roe S.M., Pearl L.H.;
"Structural basis for recruitment of translesion DNA polymerase Pol
IV/DinB to the beta-clamp.";
EMBO J. 22:5883-5892(2003).
[35] {ECO:0000244|PDB:1OK7}
X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH PEPTIDE OF
DINB, FUNCTION, AND SUBUNIT.
PubMed=14729336; DOI=10.1016/J.JMB.2003.11.049;
Burnouf D.Y., Olieric V., Wagner J., Fujii S., Reinbolt J.,
Fuchs R.P., Dumas P.;
"Structural and biochemical analysis of sliding clamp/ligand
interactions suggest a competition between replicative and translesion
DNA polymerases.";
J. Mol. Biol. 335:1187-1197(2004).
[36] {ECO:0000244|PDB:3BEP}
X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) IN COMPLEX WITH PRIMED DNA,
FUNCTION, SUBUNIT, DNA-BINDING, AND MUTAGENESIS OF ARG-24; GLN-149;
153-TYR-TYR-154 AND 272-ILE-LEU-273.
PubMed=18191219; DOI=10.1016/j.cell.2007.11.045;
Georgescu R.E., Kim S.S., Yurieva O., Kuriyan J., Kong X.P.,
O'Donnell M.;
"Structure of a sliding clamp on DNA.";
Cell 132:43-54(2008).
[37] {ECO:0000244|PDB:3D1E, ECO:0000244|PDB:3D1F, ECO:0000244|PDB:3D1G}
X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) IN COMPLEX WITH VARIOUS
PEPTIDES, SUBUNIT, AND BIOTECHNOLOGY.
PubMed=18678908; DOI=10.1073/pnas.0804754105;
Georgescu R.E., Yurieva O., Kim S.S., Kuriyan J., Kong X.P.,
O'Donnell M.;
"Structure of a small-molecule inhibitor of a DNA polymerase sliding
clamp.";
Proc. Natl. Acad. Sci. U.S.A. 105:11116-11121(2008).
[38] {ECO:0000244|PDB:5FKU, ECO:0000244|PDB:5FKV, ECO:0000244|PDB:5FKW}
STRUCTURE BY ELECTRON MICROSCOPY (7.30 ANGSTROMS) OF DNAE; DNAN; DNAQ;
DNAX WITH AND WITHOUT DNA, FUNCTION, SUBUNIT, AND DNA-BINDING.
PubMed=26499492; DOI=10.7554/eLife.11134;
Fernandez-Leiro R., Conrad J., Scheres S.H., Lamers M.H.;
"cryo-EM structures of the E. coli replicative DNA polymerase reveal
its dynamic interactions with the DNA sliding clamp, exonuclease and
tau.";
Elife 4:0-0(2015).
[39]
REVIEW.
PubMed=1575709; DOI=10.1002/bies.950140206;
O'Donnell M.;
"Accessory protein function in the DNA polymerase III holoenzyme from
E. coli.";
Bioessays 14:105-111(1992).
[40]
REVIEW.
PubMed=15952889; DOI=10.1146/annurev.biochem.73.011303.073859;
Johnson A., O'Donnell M.;
"Cellular DNA replicases: components and dynamics at the replication
fork.";
Annu. Rev. Biochem. 74:283-315(2005).
-!- 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:15466025, PubMed:16168375,
PubMed:22716942, PubMed:14592985, PubMed:14729336,
PubMed:26499492, PubMed:15952889). 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:3519609,
PubMed:2040637). 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). {ECO:0000269|PubMed:10801133,
ECO:0000269|PubMed:14592985, ECO:0000269|PubMed:14729336,
ECO:0000269|PubMed:1534562, ECO:0000269|PubMed:15466025,
ECO:0000269|PubMed:16168375, ECO:0000269|PubMed:18191219,
ECO:0000269|PubMed:1999435, ECO:0000269|PubMed:2040637,
ECO:0000269|PubMed:22716942, ECO:0000269|PubMed:26499492,
ECO:0000269|PubMed:3519609, ECO:0000269|PubMed:8576210,
ECO:0000269|PubMed:8576212, ECO:0000305|PubMed:15952889}.
-!- SUBUNIT: Forms a ring-shaped head-to-tail homodimer
(PubMed:2040637, PubMed:9927437, PubMed:1349852, PubMed:12832762,
PubMed:14592985, PubMed:14729336, PubMed:18191219,
PubMed:18678908) around DNA (PubMed:18191219), which can be opened
by the delta subunit (PubMed:9927437, PubMed:11525728). Binds
interacting factors in a hydrophobic surface cleft between domains
2 and 3, each monomer is able to bind different proteins
simultaneously (PubMed:16168375, PubMed:11525728, PubMed:14592985,
PubMed:14729336, PubMed:26499492). The beta* isoform probably
forms homotrimers which probably load onto DNA (PubMed:8576212).
The DNA polymerase III holoenzyme complex contains at least 10
different subunits 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 dimeric beta sliding clamp
processivity factor (this entry) (PubMed:15466025). The clamp
loader (also called gamma complex) assembles the beta sliding
clamp onto the primed template and plays a central role in the
organization and communication at the replication fork. The clamp
loader contains delta, delta', psi and chi, and 3 copies of either
or both of two different DnaX proteins, gamma and tau. The DNA
replisome complex has a single clamp loader (3 tau and 1 each of
delta, delta', psi and chi subunits) which binds 3 Pol III cores
(1 core on the leading strand and 2 on the lagging strand) each
with a beta sliding clamp dimer. Additional proteins in the
replisome are other copies of gamma, psi and chi, Ssb, DNA
helicase and RNA primase (PubMed:20413500, PubMed:22157955,
PubMed:26499492). The beta sliding clamp can also be part of the
RIDA complex (regulatory inactivation of DnaA), consisting of ATP-
DnaA, ADP-Hda and DNA-loaded beta clamp (PubMed:15150238,
PubMed:18977760, PubMed:22716942). Also interacts with a number of
other DNA machines such as DNA polymerases I (PubMed:11459978), II
(PubMed:1999435, PubMed:1534562), IV (PubMed:14729336) and V, DNA
mismatch repair enzyme MutS (PubMed:11459978, PubMed:11573000) and
DNA ligase (PubMed:11459978). Binds to CrfC homooligomers at the
midcell position during DNA replication (PubMed:23994470). Many
proteins that bind the beta sliding clamp have the consensus
sequence Gln-Leu[Ser/Asp]Leu-Phe (PubMed:15134440).
{ECO:0000269|PubMed:11459978, ECO:0000269|PubMed:11525728,
ECO:0000269|PubMed:11573000, ECO:0000269|PubMed:12832762,
ECO:0000269|PubMed:1349852, ECO:0000269|PubMed:14592985,
ECO:0000269|PubMed:14729336, ECO:0000269|PubMed:15134440,
ECO:0000269|PubMed:15150238, ECO:0000269|PubMed:1534562,
ECO:0000269|PubMed:15466025, ECO:0000269|PubMed:16168375,
ECO:0000269|PubMed:18191219, ECO:0000269|PubMed:18678908,
ECO:0000269|PubMed:18977760, ECO:0000269|PubMed:1999435,
ECO:0000269|PubMed:2040637, ECO:0000269|PubMed:20413500,
ECO:0000269|PubMed:22157955, ECO:0000269|PubMed:22716942,
ECO:0000269|PubMed:23994470, ECO:0000269|PubMed:26499492,
ECO:0000269|PubMed:8576212, ECO:0000269|PubMed:9927437}.
-!- INTERACTION:
Self; NbExp=9; IntAct=EBI-542385, EBI-542385;
Q47155:dinB; NbExp=2; IntAct=EBI-542385, EBI-1037359;
P10443:dnaE; NbExp=17; IntAct=EBI-542385, EBI-549111;
P03007:dnaQ; NbExp=6; IntAct=EBI-542385, EBI-549131;
P06710:dnaX; NbExp=4; IntAct=EBI-542385, EBI-549140;
P69931:hda; NbExp=9; IntAct=EBI-542385, EBI-545453;
P28630:holA; NbExp=10; IntAct=EBI-542385, EBI-549153;
P0AFX0:hpf; NbExp=2; IntAct=EBI-542385, EBI-561113;
P0AG07:rpe; NbExp=4; IntAct=EBI-542385, EBI-546020;
P05845:tnsE (xeno); NbExp=4; IntAct=EBI-542385, EBI-2434514;
P0A8E7:yajQ; NbExp=2; IntAct=EBI-542385, EBI-370752;
P77395:ybbN; NbExp=2; IntAct=EBI-542385, EBI-545297;
P0AC53:zwf; NbExp=2; IntAct=EBI-542385, EBI-555656;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23994470}.
Note=Localizes to midcell position when chromosomes are condensed
during DNA replication (PubMed:23994470).
{ECO:0000269|PubMed:23994470}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage; Named isoforms=2;
Name=Beta {ECO:0000269|PubMed:8576211};
IsoId=P0A988-1; Sequence=Displayed;
Name=Beta* {ECO:0000269|PubMed:8576211};
IsoId=P0A988-2; Sequence=VSP_059030;
Note=Beta* protein is expressed in late logarithmic/early
stationary phase and induced by UV treatment (Ref.14). Mutations
in the Shine-Dalgarno region of beta* (some silent at the amino
acid level) decrease production of beta* (Ref.15).
{ECO:0000269|PubMed:8576210, ECO:0000269|PubMed:8576211};
-!- INDUCTION: Induced 1.5-fold by hydroxyurea (PubMed:20005847). A
shorter isoform, beta* is induced by UV treatment and also at low
levels in late logarithmic/early stationary phase growth (at
protein level) (PubMed:8576210). Beta* transcription induced by
naldixic acid (PubMed:8576211). {ECO:0000269|PubMed:20005847,
ECO:0000269|PubMed:8576210, ECO:0000269|PubMed:8576211}.
-!- BIOTECHNOLOGY: Small molecules can bind to the hydrophobic cleft
and inhibit binding of various protein factors, suggesting this
may make and attractive antibiotic target (PubMed:18678908).
{ECO:0000269|PubMed:18678908}.
-!- MISCELLANEOUS: The temperature- and UV-sensitive allele dnaN159
does not grow at temperatures 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.
{ECO:0000269|PubMed:15466025}.
-!- SIMILARITY: Belongs to the beta sliding clamp family.
{ECO:0000305}.
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; J01602; AAB59150.1; -; Genomic_DNA.
EMBL; L10328; AAA62052.1; -; Genomic_DNA.
EMBL; U00096; AAC76724.1; -; Genomic_DNA.
EMBL; AP009048; BAE77593.1; -; Genomic_DNA.
EMBL; M19876; AAA23695.1; -; Genomic_DNA.
EMBL; M13822; AAA24512.1; -; Genomic_DNA.
EMBL; K02179; AAA24510.1; -; Genomic_DNA.
EMBL; X04341; CAA27869.1; -; Genomic_DNA.
PIR; A91510; DJEC3B.
RefSeq; NP_418156.1; NC_000913.3.
RefSeq; WP_000673464.1; NZ_LN832404.1.
PDB; 1JQJ; X-ray; 2.90 A; A/B=1-366.
PDB; 1JQL; X-ray; 2.50 A; A=1-366.
PDB; 1MMI; X-ray; 1.85 A; A/B=1-366.
PDB; 1OK7; X-ray; 1.65 A; A/B=1-366.
PDB; 1UNN; X-ray; 1.90 A; A/B=1-366.
PDB; 1WAI; Model; -; A/B=1-366.
PDB; 2POL; X-ray; 2.50 A; A/B=1-366.
PDB; 2XUR; X-ray; 1.90 A; A/B=1-366.
PDB; 3BEP; X-ray; 1.92 A; A/B=1-366.
PDB; 3D1E; X-ray; 1.90 A; A/B=1-366.
PDB; 3D1F; X-ray; 2.00 A; A/B=1-366.
PDB; 3D1G; X-ray; 1.64 A; A/B=1-366.
PDB; 3F1V; X-ray; 1.77 A; A/B=1-366.
PDB; 3PWE; X-ray; 2.20 A; A/B=1-366.
PDB; 3Q4J; X-ray; 2.30 A; A/B/C/D/E/F=1-366.
PDB; 3Q4K; X-ray; 2.60 A; A/B=1-366.
PDB; 3Q4L; X-ray; 1.95 A; A/B=1-366.
PDB; 3QSB; X-ray; 1.90 A; A/B=1-366.
PDB; 4K3K; X-ray; 1.85 A; A/B=1-366.
PDB; 4K3L; X-ray; 1.50 A; A/B=1-366.
PDB; 4K3M; X-ray; 1.85 A; A/B=1-366.
PDB; 4K3O; X-ray; 2.00 A; A/B=1-366.
PDB; 4K3P; X-ray; 2.15 A; A/B=1-366.
PDB; 4K3Q; X-ray; 1.85 A; A/B=1-366.
PDB; 4K3R; X-ray; 1.86 A; A/B=1-366.
PDB; 4K3S; X-ray; 1.75 A; A/B=1-366.
PDB; 4MJP; X-ray; 1.86 A; A/B=1-366.
PDB; 4MJQ; X-ray; 1.73 A; A/B=1-366.
PDB; 4MJR; X-ray; 1.62 A; A/B=1-366.
PDB; 4N94; X-ray; 1.73 A; A/B=1-366.
PDB; 4N95; X-ray; 1.80 A; A/B=1-366.
PDB; 4N96; X-ray; 1.70 A; A/B=1-366.
PDB; 4N97; X-ray; 1.97 A; A/B=1-366.
PDB; 4N98; X-ray; 1.70 A; A/B=1-366.
PDB; 4N99; X-ray; 2.30 A; A/B=1-366.
PDB; 4N9A; X-ray; 1.90 A; A/B=1-366.
PDB; 5FKU; EM; 8.34 A; B/C=1-366.
PDB; 5FKV; EM; 8.00 A; B/C=1-366.
PDB; 5FKW; EM; 7.30 A; B/C=1-366.
PDB; 5M1S; EM; 6.70 A; B/C=1-366.
PDBsum; 1JQJ; -.
PDBsum; 1JQL; -.
PDBsum; 1MMI; -.
PDBsum; 1OK7; -.
PDBsum; 1UNN; -.
PDBsum; 1WAI; -.
PDBsum; 2POL; -.
PDBsum; 2XUR; -.
PDBsum; 3BEP; -.
PDBsum; 3D1E; -.
PDBsum; 3D1F; -.
PDBsum; 3D1G; -.
PDBsum; 3F1V; -.
PDBsum; 3PWE; -.
PDBsum; 3Q4J; -.
PDBsum; 3Q4K; -.
PDBsum; 3Q4L; -.
PDBsum; 3QSB; -.
PDBsum; 4K3K; -.
PDBsum; 4K3L; -.
PDBsum; 4K3M; -.
PDBsum; 4K3O; -.
PDBsum; 4K3P; -.
PDBsum; 4K3Q; -.
PDBsum; 4K3R; -.
PDBsum; 4K3S; -.
PDBsum; 4MJP; -.
PDBsum; 4MJQ; -.
PDBsum; 4MJR; -.
PDBsum; 4N94; -.
PDBsum; 4N95; -.
PDBsum; 4N96; -.
PDBsum; 4N97; -.
PDBsum; 4N98; -.
PDBsum; 4N99; -.
PDBsum; 4N9A; -.
PDBsum; 5FKU; -.
PDBsum; 5FKV; -.
PDBsum; 5FKW; -.
PDBsum; 5M1S; -.
ProteinModelPortal; P0A988; -.
SMR; P0A988; -.
BioGrid; 4259535; 183.
ComplexPortal; CPX-1927; DNA polymerase III, beta sliding clamp processivity factor complex.
ComplexPortal; CPX-1954; Hda-beta clamp complex.
DIP; DIP-36038N; -.
IntAct; P0A988; 39.
MINT; P0A988; -.
STRING; 316385.ECDH10B_3887; -.
BindingDB; P0A988; -.
ChEMBL; CHEMBL3562169; -.
PaxDb; P0A988; -.
PRIDE; P0A988; -.
EnsemblBacteria; AAC76724; AAC76724; b3701.
EnsemblBacteria; BAE77593; BAE77593; BAE77593.
GeneID; 948218; -.
KEGG; ecj:JW3678; -.
KEGG; eco:b3701; -.
PATRIC; fig|1411691.4.peg.3002; -.
EchoBASE; EB0238; -.
EcoGene; EG10242; dnaN.
eggNOG; ENOG4105CZ8; Bacteria.
eggNOG; COG0592; LUCA.
HOGENOM; HOG000071791; -.
InParanoid; P0A988; -.
KO; K02338; -.
PhylomeDB; P0A988; -.
BioCyc; EcoCyc:EG10242-MONOMER; -.
BioCyc; MetaCyc:EG10242-MONOMER; -.
EvolutionaryTrace; P0A988; -.
PRO; PR:P0A988; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0009360; C:DNA polymerase III complex; IEA:InterPro.
GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IDA:EcoCyc.
CDD; cd00140; beta_clamp; 1.
InterPro; IPR001001; DNA_polIII_beta.
InterPro; IPR022635; DNA_polIII_beta_C.
InterPro; IPR022637; DNA_polIII_beta_cen.
InterPro; IPR022634; DNA_polIII_beta_N.
PANTHER; PTHR30478; PTHR30478; 1.
Pfam; PF00712; DNA_pol3_beta; 1.
Pfam; PF02767; DNA_pol3_beta_2; 1.
Pfam; PF02768; DNA_pol3_beta_3; 1.
PIRSF; PIRSF000804; DNA_pol_III_b; 1.
SMART; SM00480; POL3Bc; 1.
TIGRFAMs; TIGR00663; dnan; 1.
1: Evidence at protein level;
3D-structure; Alternative promoter usage; Complete proteome;
Cytoplasm; DNA replication; DNA-binding; DNA-directed DNA polymerase;
Nucleotidyltransferase; Reference proteome; Transferase.
CHAIN 1 366 Beta sliding clamp.
/FTId=PRO_0000105434.
NP_BIND 153 154 DNA. {ECO:0000305|PubMed:18191219}.
REGION 1 120 1. {ECO:0000305}.
REGION 129 243 2. {ECO:0000305}.
REGION 245 365 3. {ECO:0000305}.
BINDING 24 24 DNA. {ECO:0000305|PubMed:18191219}.
BINDING 73 73 DNA. {ECO:0000269|PubMed:18191219}.
BINDING 149 149 DNA. {ECO:0000305|PubMed:18191219}.
VAR_SEQ 1 134 Missing (in isoform Beta*).
{ECO:0000269|PubMed:8576211}.
/FTId=VSP_059030.
MUTAGEN 24 24 R->A: Mild defect in DNA replication,
impaired loading of clamp on DNA,
polymerase speed is wild-type. More
severe replication defect and very poor
clamp loading; when associated with A-
149. {ECO:0000269|PubMed:18191219}.
MUTAGEN 66 66 G->E: In dnaN159; a temperature- and UV-
sensitive mutation, displays altered DNA
polymerase usage, chronically induced SOS
response; when associated with A-174.
{ECO:0000269|PubMed:15466025}.
MUTAGEN 133 133 A->T: Reduction of synthesis of beta*,
probably due to mutation of its promoter.
{ECO:0000269|PubMed:8576211}.
MUTAGEN 135 135 M->L: 3-fold reduction of synthesis of
beta*, probably due to loss of its start
codon. {ECO:0000269|PubMed:8576211}.
MUTAGEN 146 146 M->L: No effect on synthesis of beta*.
{ECO:0000269|PubMed:8576211}.
MUTAGEN 149 149 Q->A: Mild defect in DNA replication,
impaired loading of clamp on DNA,
polymerase speed is wild-type. More
severe replication defect and very poor
clamp loading; when associated with A-24.
{ECO:0000269|PubMed:18191219}.
MUTAGEN 153 154 YY->SS: Very poor loading of clamp on
DNA, polymerase speed is wild-type.
{ECO:0000269|PubMed:18191219}.
MUTAGEN 174 174 G->A: In dnaN159; a temperature- and UV-
sensitive mutation, displays altered DNA
polymerase usage, chronically induced SOS
response; when associated with A-66.
{ECO:0000269|PubMed:15466025}.
MUTAGEN 272 273 IL->AA: Monomeric in solution, binds very
tightly to subunit delta (holA). The
monomer binds tightly to linear and
circular DNA. Cannot bind both Pol III
and IV simultaneously.
{ECO:0000269|PubMed:11525728,
ECO:0000269|PubMed:16168375,
ECO:0000269|PubMed:18191219}.
STRAND 2 6 {ECO:0000244|PDB:4K3L}.
HELIX 7 17 {ECO:0000244|PDB:4K3L}.
TURN 18 20 {ECO:0000244|PDB:4N95}.
STRAND 26 28 {ECO:0000244|PDB:1JQL}.
HELIX 29 31 {ECO:0000244|PDB:4K3L}.
STRAND 32 38 {ECO:0000244|PDB:4K3L}.
STRAND 41 47 {ECO:0000244|PDB:4K3L}.
STRAND 49 58 {ECO:0000244|PDB:4K3L}.
STRAND 66 71 {ECO:0000244|PDB:4K3L}.
HELIX 72 81 {ECO:0000244|PDB:4K3L}.
STRAND 87 93 {ECO:0000244|PDB:4K3L}.
STRAND 96 101 {ECO:0000244|PDB:4K3L}.
STRAND 104 109 {ECO:0000244|PDB:4K3L}.
HELIX 113 115 {ECO:0000244|PDB:4K3L}.
STRAND 126 131 {ECO:0000244|PDB:4K3L}.
HELIX 132 142 {ECO:0000244|PDB:4K3L}.
HELIX 143 145 {ECO:0000244|PDB:4K3L}.
HELIX 153 156 {ECO:0000244|PDB:4K3L}.
STRAND 157 163 {ECO:0000244|PDB:4K3L}.
STRAND 166 172 {ECO:0000244|PDB:4K3L}.
STRAND 174 183 {ECO:0000244|PDB:4K3L}.
STRAND 190 195 {ECO:0000244|PDB:4K3L}.
HELIX 197 205 {ECO:0000244|PDB:4K3L}.
STRAND 209 211 {ECO:0000244|PDB:3D1G}.
STRAND 213 218 {ECO:0000244|PDB:4K3L}.
STRAND 220 227 {ECO:0000244|PDB:4K3L}.
STRAND 230 235 {ECO:0000244|PDB:4K3L}.
HELIX 244 246 {ECO:0000244|PDB:4K3L}.
STRAND 254 259 {ECO:0000244|PDB:4K3L}.
HELIX 260 271 {ECO:0000244|PDB:4K3L}.
TURN 276 278 {ECO:0000244|PDB:4K3L}.
STRAND 280 286 {ECO:0000244|PDB:4K3L}.
STRAND 289 295 {ECO:0000244|PDB:4K3L}.
STRAND 301 307 {ECO:0000244|PDB:4K3L}.
STRAND 309 312 {ECO:0000244|PDB:4MJR}.
STRAND 315 320 {ECO:0000244|PDB:4K3L}.
HELIX 321 331 {ECO:0000244|PDB:4K3L}.
STRAND 334 340 {ECO:0000244|PDB:4K3L}.
STRAND 343 345 {ECO:0000244|PDB:1JQL}.
STRAND 347 351 {ECO:0000244|PDB:4K3L}.
STRAND 354 361 {ECO:0000244|PDB:4K3L}.
SEQUENCE 366 AA; 40587 MW; 7A45646F61255B5A CRC64;
MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV
QPHEPGATTV PARKFFDICR GLPEGAEIAV QLEGERMLVR SGRSRFSLST LPAADFPNLD
DWQSEVEFTL PQATMKRLIE ATQFSMAHQD VRYYLNGMLF ETEGEELRTV ATDGHRLAVC
SMPIGQSLPS HSVIVPRKGV IELMRMLDGG DNPLRVQIGS NNIRAHVGDF IFTSKLVDGR
FPDYRRVLPK NPDKHLEAGC DLLKQAFARA AILSNEKFRG VRLYVSENQL KITANNPEQE
EAEEILDVTY SGAEMEIGFN VSYVLDVLNA LKCENVRMML TDSVSSVQIE DAASQSAAYV
VMPMRL


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