DPO3B_MYCTU
ID DPO3B_MYCTU Reviewed; 402 AA.
AC P9WNU1; L0T229; O53602; Q50790;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 46.
DE RecName: Full=Beta sliding clamp;
DE Short=Beta clamp;
DE Short=Sliding clamp;
DE AltName: Full=Beta-clamp processivity factor;
DE AltName: Full=DNA polymerase III beta sliding clamp subunit;
DE AltName: Full=DNA polymerase III subunit beta;
DE AltName: Full=Mtb beta-clamp {ECO:0000303|PubMed:22545130};
GN Name=dnaN; OrderedLocusNames=Rv0002; ORFNames=MTCY10H4.0, MTV029.02;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=8733228; DOI=10.1111/j.1365-2958.1996.tb02617.x;
RA Salazar L., Fsihi H., De Rossi E., Riccardi G., Rios C., Cole S.T.,
RA Takiff H.E.;
RT "Organization of the origins of replication of the chromosomes of
RT Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium
RT tuberculosis and isolation of a functional origin from M. smegmatis.";
RL Mol. Microbiol. 20:283-293(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4] {ECO:0007744|PDB:3P16}
RP X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS), AND SUBUNIT.
RX PubMed=21219854; DOI=10.1016/j.bbrc.2011.01.027;
RA Gui W.J., Lin S.Q., Chen Y.Y., Zhang X.E., Bi L.J., Jiang T.;
RT "Crystal structure of DNA polymerase III beta sliding clamp from
RT Mycobacterium tuberculosis.";
RL Biochem. Biophys. Res. Commun. 405:272-277(2011).
RN [5] {ECO:0007744|PDB:3RB9}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 8-402, INTERACTION WITH DNAX,
RP SUBUNIT, AND DNA-BINDING.
RC STRAIN=H37Rv;
RX PubMed=22545130; DOI=10.1371/journal.pone.0035702;
RA Kukshal V., Khanam T., Chopra D., Singh N., Sanyal S., Ramachandran R.;
RT "M. tuberculosis sliding beta-clamp does not interact directly with the
RT NAD+-dependent DNA ligase.";
RL PLoS ONE 7:E35702-E35702(2012).
RN [6] {ECO:0007744|PDB:5AGU, ECO:0007744|PDB:5AGV}
RP X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) IN COMPLEX WITH ANTIBIOTICS,
RP SUBUNIT, AND ANTIBIOTIC-BINDING.
RC STRAIN=H37Rv;
RX PubMed=26045430; DOI=10.1126/science.aaa4690;
RA Kling A., Lukat P., Almeida D.V., Bauer A., Fontaine E., Sordello S.,
RA Zaburannyi N., Herrmann J., Wenzel S.C., Konig C., Ammerman N.C.,
RA Barrio M.B., Borchers K., Bordon-Pallier F., Bronstrup M., Courtemanche G.,
RA Gerlitz M., Geslin M., Hammann P., Heinz D.W., Hoffmann H., Klieber S.,
RA Kohlmann M., Kurz M., Lair C., Matter H., Nuermberger E., Tyagi S.,
RA Fraisse L., Grosset J.H., Lagrange S., Muller R.;
RT "Targeting DnaN for tuberculosis therapy using novel griselimycins.";
RL Science 348:1106-1112(2015).
CC -!- FUNCTION: Confers DNA tethering and processivity to DNA polymerases and
CC other proteins. Acts as a clamp, forming a ring around DNA (a reaction
CC catalyzed by the clamp-loading complex) which diffuses in an ATP-
CC independent manner freely and bidirectionally along dsDNA. Initially
CC characterized for its ability to contact the catalytic subunit of DNA
CC polymerase III (Pol III), a complex, multichain enzyme responsible for
CC most of the replicative synthesis in bacteria; Pol III exhibits 3'-5'
CC exonuclease proofreading activity. The beta chain is required for
CC initiation of replication as well as for processivity of DNA
CC replication (By similarity). Binds ds- and ssDNA (PubMed:22545130).
CC Binds the antibiotic griselimycin and its derivatives with high
CC affinity (1.0 x 10(-10) to 2.0 x 10(-10) M sec(-1)) (PubMed:26045430).
CC Binding occurs in a hydrophobic cleft between domains 2 and 3, which
CC have been shown to be responsible for binding DNA polymerases and other
CC DNA-modifying proteins (PubMed:26045430).
CC {ECO:0000250|UniProtKB:P0A988, ECO:0000269|PubMed:22545130,
CC ECO:0000269|PubMed:26045430}.
CC -!- SUBUNIT: Forms a ring-shaped head-to-tail homodimer (PubMed:21219854,
CC PubMed:22545130, PubMed:26045430) around DNA which binds and tethers
CC DNA polymerases and other proteins to the DNA (PubMed:22545130). The
CC DNA replisome complex has a single clamp-loading complex (3 tau and 1
CC each of delta, delta', psi and chi subunits) which binds 3 Pol III
CC cores (1 core on the leading strand and 2 on the lagging strand) each
CC with a beta sliding clamp dimer (By similarity). Additional proteins in
CC the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase
CC and RNA primase (By similarity). Interacts with the tau/gamma subunit
CC (dnaX) (PubMed:22545130). {ECO:0000250|UniProtKB:P0A988,
CC ECO:0000269|PubMed:21219854, ECO:0000269|PubMed:22545130,
CC ECO:0000269|PubMed:26045430}.
CC -!- INTERACTION:
CC P9WNU1; P9WNU1: dnaN; NbExp=2; IntAct=EBI-6410341, EBI-6410341;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P0A988}.
CC -!- MISCELLANEOUS: Strains that are resistant to griselimycin occur at a
CC very low fequency and are associated with amplification of a 10.3 kb
CC chromosomal segment containing this gene as well as the ori site,
CC suggesting antibiotic resistance may be due to overexpression of the
CC wild-type protein (PubMed:26045430). {ECO:0000269|PubMed:26045430}.
CC -!- SIMILARITY: Belongs to the beta sliding clamp family. {ECO:0000305}.
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DR EMBL; X92504; CAA63258.1; -; Genomic_DNA.
DR EMBL; AL123456; CCP42724.1; -; Genomic_DNA.
DR PIR; F70850; F70850.
DR RefSeq; NP_214516.1; NC_000962.3.
DR RefSeq; WP_003400271.1; NZ_NVQJ01000005.1.
DR PDB; 3P16; X-ray; 2.89 A; A/B/C/D/E/F=1-402.
DR PDB; 3RB9; X-ray; 3.00 A; A/B=8-402.
DR PDB; 5AGU; X-ray; 2.17 A; A/B=1-402.
DR PDB; 5AGV; X-ray; 1.93 A; A/B=1-402.
DR PDBsum; 3P16; -.
DR PDBsum; 3RB9; -.
DR PDBsum; 5AGU; -.
DR PDBsum; 5AGV; -.
DR AlphaFoldDB; P9WNU1; -.
DR SASBDB; P9WNU1; -.
DR SMR; P9WNU1; -.
DR IntAct; P9WNU1; 4.
DR STRING; 83332.Rv0002; -.
DR PaxDb; P9WNU1; -.
DR DNASU; 887092; -.
DR GeneID; 887092; -.
DR KEGG; mtu:Rv0002; -.
DR TubercuList; Rv0002; -.
DR eggNOG; COG0592; Bacteria.
DR OMA; YLIMPVR; -.
DR PhylomeDB; P9WNU1; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009360; C:DNA polymerase III complex; IEA:InterPro.
DR GO; GO:0005576; C:extracellular region; HDA:MTBBASE.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IBA:GO_Central.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR CDD; cd00140; beta_clamp; 1.
DR InterPro; IPR001001; DNA_polIII_beta.
DR InterPro; IPR022635; DNA_polIII_beta_C.
DR InterPro; IPR022637; DNA_polIII_beta_cen.
DR InterPro; IPR022634; DNA_polIII_beta_N.
DR PANTHER; PTHR30478; PTHR30478; 1.
DR Pfam; PF00712; DNA_pol3_beta; 1.
DR Pfam; PF02767; DNA_pol3_beta_2; 1.
DR Pfam; PF02768; DNA_pol3_beta_3; 1.
DR PIRSF; PIRSF000804; DNA_pol_III_b; 1.
DR SMART; SM00480; POL3Bc; 1.
DR TIGRFAMs; TIGR00663; dnan; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Cytoplasm; DNA replication;
KW DNA-binding; DNA-directed DNA polymerase; Nucleotidyltransferase;
KW Reference proteome; Transferase.
FT CHAIN 1..402
FT /note="Beta sliding clamp"
FT /id="PRO_0000105451"
FT CONFLICT 171..184
FT /note="ILGETVVLAATDRF -> SLVRRGCATDS (in Ref. 1; CAA63258)"
FT /evidence="ECO:0000305"
FT CONFLICT 192
FT /note="K -> E (in Ref. 1; CAA63258)"
FT /evidence="ECO:0000305"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 19..30
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 44..50
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 61..70
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 72..75
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 77..82
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 83..92
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 95..103
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 141..152
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 158..160
FT /evidence="ECO:0007829|PDB:3P16"
FT HELIX 162..165
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 166..172
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 175..181
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 183..192
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 194..197
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 201..207
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 208..218
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 220..222
FT /evidence="ECO:0007829|PDB:3P16"
FT STRAND 224..228
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:5AGV"
FT TURN 234..237
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 238..244
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 247..252
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 267..276
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 277..287
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 288..290
FT /evidence="ECO:0007829|PDB:5AGV"
FT TURN 292..294
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 297..302
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 305..312
FT /evidence="ECO:0007829|PDB:5AGV"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 316..323
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 325..329
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 331..335
FT /evidence="ECO:0007829|PDB:5AGV"
FT HELIX 337..346
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 349..357
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 363..368
FT /evidence="ECO:0007829|PDB:5AGV"
FT STRAND 390..395
FT /evidence="ECO:0007829|PDB:5AGV"
SQ SEQUENCE 402 AA; 42113 MW; 1AB4B6D18653B42D CRC64;
MDAATTRVGL TDLTFRLLRE SFADAVSWVA KNLPARPAVP VLSGVLLTGS DNGLTISGFD
YEVSAEAQVG AEIVSPGSVL VSGRLLSDIT RALPNKPVDV HVEGNRVALT CGNARFSLPT
MPVEDYPTLP TLPEETGLLP AELFAEAISQ VAIAAGRDDT LPMLTGIRVE ILGETVVLAA
TDRFRLAVRE LKWSASSPDI EAAVLVPAKT LAEAAKAGIG GSDVRLSLGT GPGVGKDGLL
GISGNGKRST TRLLDAEFPK FRQLLPTEHT AVATMDVAEL IEAIKLVALV ADRGAQVRME
FADGSVRLSA GADDVGRAEE DLVVDYAGEP LTIAFNPTYL TDGLSSLRSE RVSFGFTTAG
KPALLRPVSG DDRPVAGLNG NGPFPAVSTD YVYLLMPVRL PG
