EzCatDB: M00213
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DB codeM00213
RLCP classification1.15.8230.361 : Hydrolysis
CATH domainDomain 13.30.565.10 : Heat Shock Protein 90Catalytic domain
Domain 23.30.230.10 : Ribosomal Protein S5; domain 2Catalytic domain
Domain 33.40.-.-
Domain 4-.-.-.-
E.C.5.99.1.3

CATH domainRelated DB codes (homologues)
3.30.230.10 : Ribosomal Protein S5; domain 2T00244,M00048
3.30.565.10 : Heat Shock Protein 90M00048

Enzyme Name
UniProtKBKEGG

P0AES6Q9LCX5
Protein nameDNA gyrase subunit BDNA gyrase subunit BDNA topoisomerase (ATP-hydrolysing)
type II DNA topoisomerase
DNA-gyrase
deoxyribonucleate topoisomerase
deoxyribonucleic topoisomerase
topoisomerase
DNA topoisomerase II
SynonymsEC 5.99.1.3
EC 5.99.1.3
RefSeqYP_026241.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491736.1 (Protein)
NC_007779.1 (DNA/RNA sequence)

PfamPF00204 (DNA_gyraseB)
PF00986 (DNA_gyraseB_C)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical view]
PF00204 (DNA_gyraseB)
PF00986 (DNA_gyraseB_C)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical view]


UniProtKB:Accession NumberP0AES6Q9LCX5
Entry nameGYRB_ECOLIQ9LCX5_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


Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00434C00002C00434C00008C00009
CompoundMagnesiumDouble-stranded DNAATPDouble-stranded DNAADPOrthophosphate
Typedivalent metal (Ca2+, Mg2+)nucleic acidsamine group,nucleotidenucleic acidsamine group,nucleotidephosphate group/phosphate ion
ChEBI18420

15422

16761
26078
PubChem888

5957

6022
22486802
1004
              
1ei1A01UnboundUnboundAnalogue:ANPUnboundUnboundUnbound
1ei1B01UnboundUnboundAnalogue:ANPUnboundUnboundUnbound
1aj6AUnboundUnboundUnboundUnboundUnboundUnbound
1kznAUnboundUnboundUnboundUnboundUnboundUnbound
1kijA01UnboundUnboundUnboundUnboundUnboundUnbound
1kijB01UnboundUnboundUnboundUnboundUnboundUnbound
1ei1A02UnboundUnboundUnboundUnboundUnboundUnbound
1ei1B02UnboundUnboundUnboundUnboundUnboundUnbound
1kijA02UnboundUnboundUnboundUnboundUnboundUnbound
1kijB02UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature[5] & comparison with M00048
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1ei1A01GLU  42
ASN  46(magnesium binding)
LEU 115;HIS 116;GLY 117;VAL 118;GLY 119
 
1ei1B01GLU 442
ASN 446(magnesium binding)
LEU 515;HIS 516;GLY 517;VAL 518;GLY 519
 
1aj6AGLU  42
ASN  46(magnesium binding)
LEU 115;HIS 116;GLY 117;VAL 118;GLY 119
 
1kznAGLU  42
ASN  46(magnesium binding)
       ;HIS 116;GLY 117;VAL 118;GLY 119
invisible 97-115
1kijA01GLU  41
ASN  45(magnesium binding)
LEU 114;HIS 115;GLY 116;VAL 117;GLY 118
 
1kijB01GLU  41
ASN  45(magnesium binding)
LEU 114;HIS 115;GLY 116;VAL 117;GLY 118
 
1ei1A02LYS 337
 
 
 
1ei1B02LYS 737
 
 
 
1kijA02LYS 337
 
 
 
1kijB02LYS 337
 
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.627-629
[5]Fig.1B1
[16]p.9472-9473
[18]p.27
[21]Fig.63

references
[1]
PubMed ID2547660
JournalFEBS Lett
Year1989
Volume253
Pages67-70
AuthorsMcEachern F, Fisher LM
TitleRegulation of DNA supercoiling in Escherichia coli: genetic basis of a compensatory mutation in DNA gyrase.
[2]
PubMed ID1846427
JournalJ Mol Biol
Year1991
Volume217
Pages15-7
AuthorsJackson AP, Maxwell A, Wigley DB
TitlePreliminary crystallographic analysis of the ATP-hydrolysing domain of the Escherichia coli DNA gyrase B protein.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-392
Medline ID91270367
PubMed ID1646964
JournalNature
Year1991
Volume351
Pages624-9
AuthorsWigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G
TitleCrystal structure of an N-terminal fragment of the DNA gyrase B protein.
Related UniProtKBP0AES6
[4]
PubMed ID8231802
JournalMol Microbiol
Year1993
Volume9
Pages681-6
AuthorsMaxwell A
TitleThe interaction between coumarin drugs and DNA gyrase.
[5]
PubMed ID8248233
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages11232-6
AuthorsJackson AP, Maxwell A
TitleIdentifying the catalytic residue of the ATPase reaction of DNA gyrase.
[6]
PubMed ID8107146
JournalJ Mol Biol
Year1994
Volume236
Pages618-28
AuthorsCelia H, Hoermann L, Schultz P, Lebeau L, Mallouh V, Wigley DB, Wang JC, Mioskowski C, Oudet P
TitleThree-dimensional model of Escherichia coli gyrase B subunit crystallized in two-dimensions on novobiocin-linked phospholipid films.
[7]
PubMed ID7719848
JournalNat Struct Biol
Year1995
Volume2
Pages25-6
AuthorsMurzin AG
TitleA ribosomal protein module in EF-G and DNA gyrase.
[8]
PubMed ID8635474
JournalEMBO J
Year1996
Volume15
Pages1412-20
AuthorsLewis RJ, Singh OM, Smith CV, Skarzynski T, Maxwell A, Wonacott AJ, Wigley DB
TitleThe nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-220 OF MUTANT HIS-135
Medline ID97392632
PubMed ID9245398
JournalBiochemistry
Year1997
Volume36
Pages9663-73
AuthorsHoldgate GA, Tunnicliffe A, Ward WH, Weston SA, Rosenbrock G, Barth PT, Taylor IW, Pauptit RA, Timms D
TitleThe entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study.
Related PDB1aj6
Related UniProtKBP0AES6
[10]
PubMed ID9144789
JournalProteins
Year1997
Volume28
Pages41-52
AuthorsTsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O'Brien R, Ladbury JE, Wigley DB
TitleThe high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin.
[11]
PubMed ID9545289
JournalJ Biol Chem
Year1998
Volume273
Pages9586-92
AuthorsHu T, Chang S, Hsieh T
TitleIdentifying Lys359 as a critical residue for the ATP-dependent reactions of Drosophila DNA topoisomerase II.
[12]
PubMed ID9712889
JournalJ Biol Chem
Year1998
Volume273
Pages22606-14
AuthorsKampranis SC, Maxwell A
TitleConformational changes in DNA gyrase revealed by limited proteolysis.
[13]
PubMed ID9657678
JournalBiochemistry
Year1998
Volume37
Pages9658-67
AuthorsSmith CV, Maxwell A
TitleIdentification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase.
[14]
PubMed ID10575351
JournalBiochimie
Year1999
Volume81
Pages973-80
AuthorsBrino L, Bronner C, Oudet P, Mousli M
TitleIsoleucine 10 is essential for DNA gyrase B function in Escherichia coli.
[15]
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.
[16]
CommentsX-ray crystallography
PubMed ID10734094
JournalJ Biol Chem
Year2000
Volume275
Pages9468-75
AuthorsBrino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D
TitleDimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center.
Related PDB1ei1
[17]
PubMed ID10850814
JournalProtein Sci
Year2000
Volume9
Pages1035-7
AuthorsBlance SJ, Williams NL, Preston ZA, Bishara J, Smyth MS, Maxwell A
TitleTemperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein.
[18]
PubMed ID10637609
JournalTrends Biochem Sci
Year2000
Volume25
Pages24-8
AuthorsDutta R, Inouye M
TitleGHKL, an emergent ATPase/kinase superfamily.
[19]
PubMed ID11399091
JournalJ Mol Biol
Year2001
Volume309
Pages1219-31
AuthorsHeddle JG, Lu T, Zhao X, Drlica K, Maxwell A
TitlegyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity.
[20]
PubMed ID12044152
JournalBiochemistry
Year2002
Volume41
Pages7217-23
AuthorsLafitte D, Lamour V, Tsvetkov PO, Makarov AA, Klich M, Deprez P, Moras D, Briand C, Gilli R
TitleDNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose.
Related PDB1kzn
[21]
PubMed ID11850422
JournalJ Biol Chem
Year2002
Volume277
Pages18947-53
AuthorsLamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D
TitleAn open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
Related PDB1kij
[22]
PubMed ID12018484
JournalJ Biomol NMR
Year2002
Volume22
Pages369-70
AuthorsBellanda M, Peggion E, Otting G, Weigelt J, Perdona E, Domenici E, Marchioro C, Mammi S
TitleBackbone 1H, 13C and 15N resonance assignment of the N-terminal 24 kDa fragment of the gyrase B subunit from E. coli.
[23]
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.
[24]
PubMed ID12604539
JournalAntimicrob Agents Chemother
Year2003
Volume47
Pages1037-46
AuthorsGross CH, Parsons JD, Grossman TH, Charifson PS, Bellon S, Jernee J, Dwyer M, Chambers SP, Markland W, Botfield M, Raybuck SA
TitleActive-site residues of Escherichia coli DNA gyrase required in coupling ATP hydrolysis to DNA supercoiling and amino acid substitutions leading to novobiocin resistance.

comments
This protein is B subunit of DNA-gyrase, which catalyzes ATP hydrolysis. The A subunit of this enzyme catalyzes DNA brekage and religation (see M00137).
PDB structure, 1ei1, corresponds to the N-terminal half of the B subunit of DNA-gyrase. The other region, C-terminal half of the B subunit is responsible for the interaction with DNA and the A subunit, according to the literature [19].
According to the literature [13] & [18], the reaction proceeds as follows;
(1) Glu42 (of 1ei1) acts as a general base, to activate a water molecule, which must be in-line for a nucleophilic attack on the gamma-phosphate of ATP. Lys337 may stabilize the activated water during this reaction.
(2) Lys337 stabilizes the transition-state, along with mainchain amide of resdiues 115-119. Magnesium ion, possibly bound to Asn46, stabilizes the transition-state.

createdupdated
2004-04-252009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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