EzCatDB: M00137

DB codeM00137
CATH domainDomain 13.90.199.10Catalytic domain
Domain 23.30.1360.40
Domain 31.10.268.10
Domain 42.-.-.-
E.C.5.99.1.3
CSA1ab4

CATH domainRelated DB codes (homologues)
1.10.268.10M00048
3.30.1360.40M00048
3.90.199.10M00048

Enzyme Name
Swiss-protKEGG

P0AES4Q9LCX6
Protein nameDNA gyrase subunit A
DNA topoisomerase (ATP-hydrolysing)
type II DNA topoisomerase
DNA-gyrase
deoxyribonucleate topoisomerase
deoxyribonucleic topoisomerase
topoisomerase
DNA topoisomerase II
SynonymsEC 5.99.1.3
Gyrase subunit A


Swiss-prot:Accession NumberP0AES4Q9LCX6
Entry nameGYRA_ECOLIQ9LCX6_THETH
ActivityATP-dependent breakage, passage and rejoining of double-stranded DNA.ATP-dependent breakage, passage and rejoining of double-stranded DNA.
SubunitMade up of two chains. The A chain is responsible for DNA breakage and rejoining, the B chain catalyzes ATP hydrolysis. The enzyme forms an A2B2 tetramer.
Subcellular location

Cofactor



CofactorsSubstratesProducts
KEGG-idC00305C00434C00002C00434C00008C00009
CompoundMagnesiumDouble-stranded DNAATPDouble-stranded DNAADPOrthophosphate
Typedivalent metal (Ca2+, Mg2+)nucleic acidsamine group,nucleotidenucleic acidsamine group,nucleotidephosphate group/phosphate ion
1ab4A01UnboundUnboundUnboundUnboundUnboundUnbound
1ab4A02UnboundUnboundUnboundUnboundUnboundUnbound
1ab4A03UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0AES4 & literature [19]
pdbCatalytic residues
1ab4A01ARG 32;HIS 78;TYR 122
1ab4A02
1ab4A03

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[19]Fig.91

references
[1]
PubMed ID225107
JournalCold Spring Harb Symp Quant Biol
Year1979
Volume43 Pt 1
Pages35-40
AuthorsGellert M, Mizuuchi K, O'Dea MH, Ohmori H, Tomizawa J
TitleDNA gyrase and DNA supercoiling.
[2]
PubMed ID225110
JournalCold Spring Harb Symp Quant Biol
Year1979
Volume43 Pt 1
Pages41-52
AuthorsPeebles CL, Higgins NP, Kreuzer KN, Morrison A, Brown PO, Sugino A, Cozzarelli NR
TitleStructure and activities of Escherichia coli DNA gyrase.
[3]
PubMed ID2153834
JournalJ Mol Biol
Year1990
Volume211
Pages211-20
AuthorsKrueger S, Zaccai G, Wlodawer A, Langowski J, O'Dea M, Maxwell A, Gellert M
TitleNeutron and light-scattering studies of DNA gyrase and its complex with DNA.
[4]
PubMed ID2172550
JournalJ Mol Biol
Year1990
Volume215
Pages493-5
AuthorsReece RJ, Dauter Z, Wilson KS, Maxwell A, Wigley DB
TitlePreliminary crystallographic analysis of the breakage-reunion domain of the Escherichia coli DNA gyrase A protein.
[5]
PubMed ID1327123
JournalBiochemistry
Year1992
Volume31
Pages9642-6
AuthorsCullis PM, Maxwell A, Weiner DP
TitleEnergy coupling in DNA gyrase: a thermodynamic limit to the extent of DNA supercoiling.
[6]
PubMed ID8538787
JournalNature
Year1996
Volume379
Pages225-32
AuthorsBerger JM, Gamblin SJ, Harrison SC, Wang JC
TitleStructure and mechanism of DNA topoisomerase II.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522
Medline ID97422287
PubMed ID9278055
JournalNature
Year1997
Volume388
Pages903-6
AuthorsMorais Cabral JH, Jackson AP, Smith CV, Shikotra N, Maxwell A, Liddington RC
TitleCrystal structure of the breakage-reunion domain of DNA gyrase.
Related PDB1ab4
Related Swiss-protP0AES4
[8]
PubMed ID9712889
JournalJ Biol Chem
Year1998
Volume273
Pages22606-14
AuthorsKampranis SC, Maxwell A
TitleConformational changes in DNA gyrase revealed by limited proteolysis.
[9]
PubMed ID9685374
JournalJ Biol Chem
Year1998
Volume273
Pages20252-60
AuthorsLiu Q, Wang JC
TitleIdentification of active site residues in the "GyrA" half of yeast DNA topoisomerase II.
[10]
PubMed ID9437427
JournalNat Struct Biol
Year1998
Volume5
Pages31-6
AuthorsKlabunde T, Sharma S, Telenti A, Jacobs WR Jr, Sacchettini JC
TitleCrystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.
[11]
PubMed ID10521257
JournalBiochemistry
Year1999
Volume38
Pages13502-11
AuthorsWilliams NL, Maxwell A
TitleProbing the two-gate mechanism of DNA gyrase using cysteine cross-linking.
[12]
PubMed ID10571989
JournalBiochemistry
Year1999
Volume38
Pages14157-64
AuthorsWilliams NL, Maxwell A
TitleLocking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis.
[13]
PubMed ID10356321
JournalJ Mol Biol
Year1999
Volume289
Pages447-58
AuthorsAshizawa Y, Yokochi T, Ogata Y, Shobuike Y, Kato J, Ikeda H
TitleMechanism of DNA gyrase-mediated illegitimate recombination: characterization of Escherichia coli gyrA mutations that confer hyper-recombination phenotype.
[14]
PubMed ID10543963
JournalJ Mol Biol
Year1999
Volume293
Pages733-44
AuthorsKampranis SC, Howells AJ, Maxwell A
TitleThe interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes.
[15]
PubMed ID10411889
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages8414-9
AuthorsKampranis SC, Bates AD, Maxwell A
TitleA model for the mechanism of strand passage by DNA gyrase.
[16]
PubMed ID11451702
JournalAntimicrob Agents Chemother
Year2001
Volume45
Pages2378-80
AuthorsFriedman SM, Lu T, Drlica K
TitleMutation in the DNA gyrase A Gene of Escherichia coli that expands the quinolone resistance-determining region.
[17]
PubMed ID11408229
JournalAntimicrob Agents Chemother
Year2001
Volume45
Pages2098-105
AuthorsMaurin M, Abergel C, Raoult D
TitleDNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp.
[18]
PubMed ID11469868
JournalJ Mol Biol
Year2001
Volume311
Pages195-203
AuthorsSissi C, Perdona E, Domenici E, Feriani A, Howells AJ, Maxwell A, Palumbo M
TitleCiprofloxacin affects conformational equilibria of DNA gyrase A in the presence of magnesium ions.
[19]
PubMed ID12051843
JournalJ Mol Biol
Year2002
Volume318
Pages361-71
AuthorsNoble CG, Maxwell A
TitleThe role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism.

comments
DNA gyrase is a prokaryotic topoisomerase type II, which relaxes supercoiled DNA. This protein is A subunit of DNA-gyrase, which catalyzes DNA breakage and religation. The B subunit of this enzyme catalyzes hydrolysis of ATP. (see M00213 in EzCatDB).
According to the literature [19], this A subunit of the enzyme seems to catalyzes the DNA breakage in cooperation with the C-terminal domain of the B subunit.

createdupdated
2004-04-232009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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