GYRA_MYCLE
ID GYRA_MYCLE Reviewed; 1273 AA.
AC Q57532; Q50209; Q9CDF2;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 27-APR-2001, sequence version 2.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=DNA gyrase subunit A {ECO:0000255|HAMAP-Rule:MF_01897};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01897};
DE Contains:
DE RecName: Full=Mle GyrA intein;
GN Name=gyrA {ECO:0000255|HAMAP-Rule:MF_01897}; OrderedLocusNames=ML0006;
OS Mycobacterium leprae (strain TN).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium.
OX NCBI_TaxID=272631;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8622949; DOI=10.1073/pnas.93.8.3410;
RA Fsihi H., Vincent V., Cole S.T.;
RT "Homing events in the gyrA gene of some mycobacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:3410-3415(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=TN;
RX PubMed=11234002; DOI=10.1038/35059006;
RA Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R.,
RA Wheeler P.R., Honore N., Garnier T., Churcher C.M., Harris D.E.,
RA Mungall K.L., Basham D., Brown D., Chillingworth T., Connor R.,
RA Davies R.M., Devlin K., Duthoy S., Feltwell T., Fraser A., Hamlin N.,
RA Holroyd S., Hornsby T., Jagels K., Lacroix C., Maclean J., Moule S.,
RA Murphy L.D., Oliver K., Quail M.A., Rajandream M.A., Rutherford K.M.,
RA Rutter S., Seeger K., Simon S., Simmonds M., Skelton J., Squares R.,
RA Squares S., Stevens K., Taylor K., Whitehead S., Woodward J.R.,
RA Barrell B.G.;
RT "Massive gene decay in the leprosy bacillus.";
RL Nature 409:1007-1011(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 75-114.
RX PubMed=8540734; DOI=10.1128/aac.39.9.2145;
RA Guillemin I., Cambau E., Jarlier V.;
RT "Sequences of conserved region in the A subunit of DNA gyrase from nine
RT species of the genus Mycobacterium: phylogenetic analysis and implication
RT for intrinsic susceptibility to quinolones.";
RL Antimicrob. Agents Chemother. 39:2145-2149(1995).
RN [4]
RP FUNCTION, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=17325221; DOI=10.1128/aac.01282-06;
RA Matrat S., Petrella S., Cambau E., Sougakoff W., Jarlier V., Aubry A.;
RT "Expression and purification of an active form of the Mycobacterium leprae
RT DNA gyrase and its inhibition by quinolones.";
RL Antimicrob. Agents Chemother. 51:1643-1648(2007).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner to
CC modulate DNA topology and maintain chromosomes in an underwound state
CC (PubMed:17325221). Negative supercoiling favors strand separation, and
CC DNA replication, transcription, recombination and repair, all of which
CC involve strand separation. Also able to catalyze the interconversion of
CC other topological isomers of dsDNA rings, including catenanes and
CC knotted rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC Rule:MF_01897, ECO:0000269|PubMed:17325221}.
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_01897};
CC -!- ACTIVITY REGULATION: DNA supercoiling is inhibited by fluoroquinolones;
CC IC(50) 1 ug/ml for sitafloxacin. {ECO:0000269|PubMed:17325221}.
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC (PubMed:17325221). In the heterotetramer, GyrA contains the active site
CC tyrosine that forms a transient covalent intermediate with the DNA,
CC while GyrB binds cofactors catalyzes ATP hydrolysis.
CC {ECO:0000255|HAMAP-Rule:MF_01897, ECO:0000269|PubMed:17325221}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
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_01897}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrA/ParC subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC29514.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; Z70722; CAA94713.1; -; Genomic_DNA.
DR EMBL; Z68206; CAA92430.1; -; Genomic_DNA.
DR EMBL; AL583917; CAC29514.1; ALT_FRAME; Genomic_DNA.
DR EMBL; X87124; CAA60608.1; -; Genomic_DNA.
DR PIR; F86909; F86909.
DR PIR; T10006; T10006.
DR RefSeq; WP_010907459.1; NC_002677.1.
DR AlphaFoldDB; Q57532; -.
DR SMR; Q57532; -.
DR STRING; 272631.ML0006; -.
DR MEROPS; N10.001; -.
DR EnsemblBacteria; CAC29514; CAC29514; CAC29514.
DR KEGG; mle:ML0006; -.
DR Leproma; ML0006; -.
DR eggNOG; COG0188; Bacteria.
DR eggNOG; COG1372; Bacteria.
DR HOGENOM; CLU_002977_10_0_11; -.
DR Proteomes; UP000000806; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0034335; F:DNA negative supercoiling activity; IDA:UniProtKB.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR CDD; cd00187; TOP4c; 1.
DR Gene3D; 1.10.268.10; -; 1.
DR Gene3D; 2.120.10.90; -; 1.
DR Gene3D; 3.10.28.10; -; 1.
DR Gene3D; 3.90.199.10; -; 2.
DR InterPro; IPR006691; GyrA/parC_rep.
DR InterPro; IPR035516; Gyrase/topoIV_suA_C.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_2.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013758; Topo_IIA_A/C_ab.
DR InterPro; IPR013757; Topo_IIA_A_a_sf.
DR InterPro; IPR002205; Topo_IIA_dom_A.
DR Pfam; PF03989; DNA_gyraseA_C; 6.
DR Pfam; PF00521; DNA_topoisoIV; 2.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SMART; SM00434; TOP4c; 1.
DR SUPFAM; SSF101904; SSF101904; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
DR SUPFAM; SSF56719; SSF56719; 2.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Autocatalytic cleavage; Cytoplasm; DNA-binding; Isomerase;
KW Nucleotide-binding; Protein splicing; Reference proteome; Topoisomerase.
FT CHAIN 1..130
FT /note="DNA gyrase subunit A, 1st part"
FT /evidence="ECO:0000250"
FT /id="PRO_0000034807"
FT CHAIN 131..550
FT /note="Mle GyrA intein"
FT /evidence="ECO:0000250"
FT /id="PRO_0000034808"
FT CHAIN 551..1273
FT /note="DNA gyrase subunit A, 2nd part"
FT /evidence="ECO:0000250"
FT /id="PRO_0000034809"
FT DOMAIN 256..396
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT MOTIF 958..964
FT /note="GyrA-box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT ACT_SITE 130
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT CONFLICT 267
FT /note="F -> S (in Ref. 1; CAA94713/CAA92430)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1273 AA; 141218 MW; 4B6FFBB5BD7AEF53 CRC64;
MTDITLPPGD GSIQRVEPVD IQQEMQRSYI DYAMSVIVGR ALPEVRDGLK PVHRRVLYAM
LDSGFRPDRS HAKSARSVAE TMGNYHPHGD ASIYDTLVRM AQPWSLRYPL VDGQGNFGSP
GNDPPAAMRY CVSGNSLVRL LFGKSIRIGD IVTGAQFNSD NPIDLKVLDR HGNPVVADYL
FHSGEHQTYT VRTTEGYEIT GTSNHPLLCL VNVGGIPTLL WKLIGEIRSG DYVVLQRIPP
VEFGPADWYS TMEALLFGAF ISGGFVFQDH AGFNSLDRDY FTMVVNAYDT VVGGLRCISS
RITVSGSTLL ELDVYNLIEF KKTRLSGLCG QRSADKLVPD WLWHSPSTVK RAFLQALFEG
EGFSSILSRN IIEISYSTLS ERLAADVQQM LLEFGVVSER YCHTVNEYKV VIANRAQVEM
FFTQVGFGVT KQAKLIRDVV SMSPCVGMDI NCVPGLATFI RKHCDNRWVE EDSFNQHNVD
CVQHWHHHSA EIVGHIADPD IRAIVTDLTD GRFYYARVAS VTDTGIQPVF SLHVDTEDHS
FLTNGFISHN TEARLTPLAM EMLREIDEET VDFISNYDGR VQEPMVLPSR FPNLLANGSG
GIAVGMATNI PPHNLYELAD AVFWCLENHD ADEETMLVAV MERVKGPDFP TAGLIVGSQG
IADAYKTGRG SIRIRGVVEV EEDSRGRTSL VITELPYQVN HDNFITSIAE QVRTGRLAGI
SNVEDQGSDR VGVRIVIEIK RDAVAKVVLN NLYKHTQLQT SFGANMLSIV DGVPRTLRLD
QMICYYVEHQ LDVIVRRTTY RLRKANERAH ILRGLVKALD ALDEVITLIR ASQTVDIARV
GVVELLDIDD IQAQAILDMQ LRRLAALERQ RIIDDLAKIE VEIADLGDIL AKPERRRGII
RNELTEIAEK YGDDRRTRII AVDGDVNDED LIAREEVVVT ITETGYAKRT KTDLYRSQKR
GGKGVQGAGL KQDDIVRHFF VCSTHDWILF FTTQGRVYRA KAYELPEASR TARGQHVANL
LAFQPEERIA QVIQIRSYED APYLVLATRA GLVKKSKLTD FDSNRSGGIV AINLRDNDEL
VGAVLCAADG DLLLVSANGQ SIRFSATDEA LRPMGRATSG VQGMRFNADD RLLSLNVVRE
DTYLLVATSG GYAKRTSIEE YPMQGRGGKG VLTVMYDRRR GSLVGAIVVD EDSELYAITS
GGGVIRTTAR QVRQAGRQTK GVRLMNLGEG DTLLAIARNA EESADGVSVK VMISRSRVLS
FFGSDSNTSP DRT
