GYRB_MYCS2
ID GYRB_MYCS2 Reviewed; 675 AA.
AC A0QNE0; I7FVC1; P48355; Q59555;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898};
GN OrderedLocusNames=MSMEG_0005, MSMEI_0007;
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, FUNCTION,
RP SUBUNIT, AND ACTIVITY REGULATION.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=8878580; DOI=10.1128/aac.40.9.2054;
RA Revel-Viravau V., Truong Q.C., Moreau N., Jarlier V., Sougakoff W.;
RT "Sequence analysis, purification, and study of inhibition by 4-quinolones
RT of the DNA gyrase from Mycobacterium smegmatis.";
RL Antimicrob. Agents Chemother. 40:2054-2061(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT mutations or sequencing errors?";
RL Genome Biol. 8:R20.1-R20.9(2007).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=18955433; DOI=10.1101/gr.081901.108;
RA Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT and a new MS-based protocol.";
RL Genome Res. 19:128-135(2009).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 9-255 IN COMPLEX WITH
RP AMINOPYRAZINAMIDE, AND ACTIVITY REGULATION.
RX PubMed=23268609; DOI=10.1021/cb300510w;
RA Shirude P.S., Madhavapeddi P., Tucker J.A., Murugan K., Patil V.,
RA Basavarajappa H., Raichurkar A.V., Humnabadkar V., Hussein S., Sharma S.,
RA Ramya V.K., Narayan C.B., Balganesh T.S., Sambandamurthy V.K.;
RT "Aminopyrazinamides: novel and specific GyrB inhibitors that kill
RT replicating and nonreplicating Mycobacterium tuberculosis.";
RL ACS Chem. Biol. 8:519-523(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 19-212 AND 247-255 IN COMPLEX
RP WITH PYRROLAMIDE, AND ACTIVITY REGULATION.
RX PubMed=24126580; DOI=10.1128/aac.01751-13;
RA P S.H., Solapure S., Mukherjee K., Nandi V., Waterson D., Shandil R.,
RA Balganesh M., Sambandamurthy V.K., Raichurkar A.K., Deshpande A., Ghosh A.,
RA Awasthy D., Shanbhag G., Sheikh G., McMiken H., Puttur J., Reddy J.,
RA Werngren J., Read J., Kumar M., R M., Chinnapattu M., Madhavapeddi P.,
RA Manjrekar P., Basu R., Gaonkar S., Sharma S., Hoffner S., Humnabadkar V.,
RA Subbulakshmi V., Panduga V.;
RT "Optimization of pyrrolamides as mycobacterial GyrB ATPase inhibitors:
RT structure-activity relationship and in vivo efficacy in a mouse model of
RT tuberculosis.";
RL Antimicrob. Agents Chemother. 58:61-70(2014).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner
CC (PubMed:8878580) to modulate DNA topology and maintain chromosomes in
CC an underwound state. Negative supercoiling favors strand separation,
CC and DNA replication, transcription, recombination and repair, all of
CC which involve strand separation. Also able to catalyze the
CC interconversion of other topological isomers of dsDNA rings, including
CC catenanes and knotted rings. Type II topoisomerases break and join 2
CC DNA strands simultaneously in an ATP-dependent manner.
CC {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:8878580}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-Rule:MF_01898};
CC -!- ACTIVITY REGULATION: Inhibited by 4-quinoline drugs (nalidixic acid,
CC ciprofloxacin, ofloxacin), although it is much less sensitive than the
CC corresponding enzyme from E.coli (PubMed:8878580). GyrB intrinsic
CC ATPase activity inhibited by aminopyrazinamide and pyrrolamide
CC derivatives (PubMed:23268609, PubMed:24126580).
CC {ECO:0000269|PubMed:23268609, ECO:0000269|PubMed:24126580,
CC ECO:0000269|PubMed:8878580}.
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC (PubMed:8878580). In the heterotetramer, GyrA contains the active site
CC tyrosine that forms a transient covalent intermediate with DNA, while
CC GyrB binds cofactors and catalyzes ATP hydrolysis. {ECO:0000255|HAMAP-
CC Rule:MF_01898, ECO:0000269|PubMed:8878580}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming
CC negative supercoils. Not all organisms have 2 type II topoisomerases;
CC in organisms with a single type II topoisomerase this enzyme also has
CC to decatenate newly replicated chromosomes. {ECO:0000255|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; X94224; CAA63917.1; -; Genomic_DNA.
DR EMBL; CP000480; ABK72750.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP36492.1; -; Genomic_DNA.
DR RefSeq; WP_003891333.1; NZ_SIJM01000001.1.
DR RefSeq; YP_884428.1; NC_008596.1.
DR PDB; 4B6C; X-ray; 2.20 A; A/B=9-255.
DR PDB; 4BAE; X-ray; 2.35 A; A/B/C/D=19-212, A/B/C/D=247-255.
DR PDB; 6ZT3; X-ray; 1.56 A; A=1-427.
DR PDB; 6ZT5; X-ray; 2.20 A; C=1-427.
DR PDBsum; 4B6C; -.
DR PDBsum; 4BAE; -.
DR PDBsum; 6ZT3; -.
DR PDBsum; 6ZT5; -.
DR AlphaFoldDB; A0QNE0; -.
DR SMR; A0QNE0; -.
DR STRING; 246196.MSMEI_0007; -.
DR ChEMBL; CHEMBL6059; -.
DR PRIDE; A0QNE0; -.
DR EnsemblBacteria; ABK72750; ABK72750; MSMEG_0005.
DR EnsemblBacteria; AFP36492; AFP36492; MSMEI_0007.
DR GeneID; 66738197; -.
DR KEGG; msg:MSMEI_0007; -.
DR KEGG; msm:MSMEG_0005; -.
DR PATRIC; fig|246196.19.peg.5; -.
DR eggNOG; COG0187; Bacteria.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0034335; F:DNA negative supercoiling activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Direct protein sequencing;
KW DNA-binding; Isomerase; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome; Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8878580"
FT CHAIN 2..675
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000293599"
FT DOMAIN 453..567
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 459
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 532
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 532
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 534
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 484
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 487
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 442
FT /note="L -> S (in Ref. 1; CAA63917)"
FT /evidence="ECO:0000305"
FT CONFLICT 507
FT /note="T -> R (in Ref. 1; CAA63917)"
FT /evidence="ECO:0000305"
FT HELIX 14..16
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 22..28
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 30..34
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 39..58
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 64..69
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 109..113
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 124..130
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 132..141
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 144..151
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 168..175
FT /evidence="ECO:0007829|PDB:6ZT3"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 187..200
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 205..210
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 256..264
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 270..273
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 276..282
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 285..297
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 300..305
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 315..334
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 347..351
FT /evidence="ECO:0007829|PDB:6ZT3"
FT STRAND 354..364
FT /evidence="ECO:0007829|PDB:6ZT3"
FT TURN 369..372
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 378..398
FT /evidence="ECO:0007829|PDB:6ZT3"
FT HELIX 400..422
FT /evidence="ECO:0007829|PDB:6ZT3"
SQ SEQUENCE 675 AA; 74512 MW; 68A9B7F98BE07951 CRC64;
MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV DNAVDEAMAG
FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM TQLHAGGKFD GETYAVSGGL
HGVGVSVVNA LSTRLEATVL RDGYEWFQYY DRSVPGKLKQ GGETKETGTT IRFWADPEIF
ETTDYNFETV ARRLQEMAFL NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA
TGPSKVKHRV FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES
VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI REGLAAVISV
KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP AEAKTVVNKA VSSAQARIAA
RKARELVRRK SATDIGGLPG KLADCRSTDP SKSELYVVEG DSAGGSAKSG RDSMFQAILP
LRGKIINVEK ARIDRVLKNT EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI
STLLLTLLFR FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK
INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI LMGEDVEARR
SFITRNAKDV RFLDV
