DB code: M00213

RLCP classification 1.15.8230.361 : Hydrolysis
CATH domain 3.30.565.10 : Heat Shock Protein 90 Catalytic domain
3.30.230.10 : Ribosomal Protein S5; domain 2 Catalytic domain
3.40.-.- :
-.-.-.- :
E.C. 5.99.1.3
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AES6 DNA gyrase subunit B
EC 5.99.1.3
YP_026241.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491736.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00204 (DNA_gyraseB)
PF00986 (DNA_gyraseB_C)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical View]
Q9LCX5 DNA gyrase subunit B
EC 5.99.1.3
PF00204 (DNA_gyraseB)
PF00986 (DNA_gyraseB_C)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical View]

KEGG enzyme name
DNA topoisomerase (ATP-hydrolysing)
type II DNA topoisomerase
DNA-gyrase
deoxyribonucleate topoisomerase
deoxyribonucleic topoisomerase
topoisomerase
DNA topoisomerase II

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0AES6 GYRB_ECOLI ATP-dependent breakage, passage and rejoining of double-stranded DNA. Made 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.
Q9LCX5 Q9LCX5_THETH ATP-dependent breakage, passage and rejoining of double-stranded DNA.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00434 C00002 C00434 C00008 C00009
E.C.
Compound Magnesium Double-stranded DNA ATP Double-stranded DNA ADP Orthophosphate
Type divalent metal (Ca2+, Mg2+) nucleic acids amine group,nucleotide nucleic acids amine group,nucleotide phosphate group/phosphate ion
ChEBI 18420
15422
16761
26078
PubChem 888
5957
6022
1004
22486802
1ei1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:ANP Unbound Unbound Unbound
1ei1B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:ANP Unbound Unbound Unbound
1aj6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1kznA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1kijA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1kijB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ei1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ei1B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1kijA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1kijB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature[5] & comparison with M00048

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ei1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 42 ASN 46(magnesium binding) LEU 115;HIS 116;GLY 117;VAL 118;GLY 119
1ei1B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 442 ASN 446(magnesium binding) LEU 515;HIS 516;GLY 517;VAL 518;GLY 519
1aj6A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 42 ASN 46(magnesium binding) LEU 115;HIS 116;GLY 117;VAL 118;GLY 119
1kznA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 42 ASN 46(magnesium binding) ;HIS 116;GLY 117;VAL 118;GLY 119 invisible 97-115
1kijA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 41 ASN 45(magnesium binding) LEU 114;HIS 115;GLY 116;VAL 117;GLY 118
1kijB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 41 ASN 45(magnesium binding) LEU 114;HIS 115;GLY 116;VAL 117;GLY 118
1ei1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 337
1ei1B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 737
1kijA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 337
1kijB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 337

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.627-629
[5]
Fig.1B 1
[16]
p.9472-9473
[18]
p.27
[21]
Fig.6 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 2547660
Journal FEBS Lett
Year 1989
Volume 253
Pages 67-70
Authors McEachern F, Fisher LM
Title Regulation of DNA supercoiling in Escherichia coli: genetic basis of a compensatory mutation in DNA gyrase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1846427
Journal J Mol Biol
Year 1991
Volume 217
Pages 15-7
Authors Jackson AP, Maxwell A, Wigley DB
Title Preliminary crystallographic analysis of the ATP-hydrolysing domain of the Escherichia coli DNA gyrase B protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-392
Medline ID 91270367
PubMed ID 1646964
Journal Nature
Year 1991
Volume 351
Pages 624-9
Authors Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G
Title Crystal structure of an N-terminal fragment of the DNA gyrase B protein.
Related PDB
Related UniProtKB P0AES6
[4]
Resource
Comments
Medline ID
PubMed ID 8231802
Journal Mol Microbiol
Year 1993
Volume 9
Pages 681-6
Authors Maxwell A
Title The interaction between coumarin drugs and DNA gyrase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8248233
Journal Proc Natl Acad Sci U S A
Year 1993
Volume 90
Pages 11232-6
Authors Jackson AP, Maxwell A
Title Identifying the catalytic residue of the ATPase reaction of DNA gyrase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8107146
Journal J Mol Biol
Year 1994
Volume 236
Pages 618-28
Authors Celia H, Hoermann L, Schultz P, Lebeau L, Mallouh V, Wigley DB, Wang JC, Mioskowski C, Oudet P
Title Three-dimensional model of Escherichia coli gyrase B subunit crystallized in two-dimensions on novobiocin-linked phospholipid films.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 7719848
Journal Nat Struct Biol
Year 1995
Volume 2
Pages 25-6
Authors Murzin AG
Title A ribosomal protein module in EF-G and DNA gyrase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8635474
Journal EMBO J
Year 1996
Volume 15
Pages 1412-20
Authors Lewis RJ, Singh OM, Smith CV, Skarzynski T, Maxwell A, Wonacott AJ, Wigley DB
Title The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-220 OF MUTANT HIS-135
Medline ID 97392632
PubMed ID 9245398
Journal Biochemistry
Year 1997
Volume 36
Pages 9663-73
Authors Holdgate GA, Tunnicliffe A, Ward WH, Weston SA, Rosenbrock G, Barth PT, Taylor IW, Pauptit RA, Timms D
Title The 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 PDB 1aj6
Related UniProtKB P0AES6
[10]
Resource
Comments
Medline ID
PubMed ID 9144789
Journal Proteins
Year 1997
Volume 28
Pages 41-52
Authors Tsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O'Brien R, Ladbury JE, Wigley DB
Title The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9545289
Journal J Biol Chem
Year 1998
Volume 273
Pages 9586-92
Authors Hu T, Chang S, Hsieh T
Title Identifying Lys359 as a critical residue for the ATP-dependent reactions of Drosophila DNA topoisomerase II.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9712889
Journal J Biol Chem
Year 1998
Volume 273
Pages 22606-14
Authors Kampranis SC, Maxwell A
Title Conformational changes in DNA gyrase revealed by limited proteolysis.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9657678
Journal Biochemistry
Year 1998
Volume 37
Pages 9658-67
Authors Smith CV, Maxwell A
Title Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10575351
Journal Biochimie
Year 1999
Volume 81
Pages 973-80
Authors Brino L, Bronner C, Oudet P, Mousli M
Title Isoleucine 10 is essential for DNA gyrase B function in Escherichia coli.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10543963
Journal J Mol Biol
Year 1999
Volume 293
Pages 733-44
Authors Kampranis SC, Howells AJ, Maxwell A
Title The interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10734094
Journal J Biol Chem
Year 2000
Volume 275
Pages 9468-75
Authors Brino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D
Title Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center.
Related PDB 1ei1
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10850814
Journal Protein Sci
Year 2000
Volume 9
Pages 1035-7
Authors Blance SJ, Williams NL, Preston ZA, Bishara J, Smyth MS, Maxwell A
Title Temperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10637609
Journal Trends Biochem Sci
Year 2000
Volume 25
Pages 24-8
Authors Dutta R, Inouye M
Title GHKL, an emergent ATPase/kinase superfamily.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11399091
Journal J Mol Biol
Year 2001
Volume 309
Pages 1219-31
Authors Heddle JG, Lu T, Zhao X, Drlica K, Maxwell A
Title gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12044152
Journal Biochemistry
Year 2002
Volume 41
Pages 7217-23
Authors Lafitte D, Lamour V, Tsvetkov PO, Makarov AA, Klich M, Deprez P, Moras D, Briand C, Gilli R
Title DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose.
Related PDB 1kzn
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11850422
Journal J Biol Chem
Year 2002
Volume 277
Pages 18947-53
Authors Lamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D
Title An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
Related PDB 1kij
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12018484
Journal J Biomol NMR
Year 2002
Volume 22
Pages 369-70
Authors Bellanda M, Peggion E, Otting G, Weigelt J, Perdona E, Domenici E, Marchioro C, Mammi S
Title Backbone 1H, 13C and 15N resonance assignment of the N-terminal 24 kDa fragment of the gyrase B subunit from E. coli.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12051843
Journal J Mol Biol
Year 2002
Volume 318
Pages 361-71
Authors Noble CG, Maxwell A
Title The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12604539
Journal Antimicrob Agents Chemother
Year 2003
Volume 47
Pages 1037-46
Authors Gross CH, Parsons JD, Grossman TH, Charifson PS, Bellon S, Jernee J, Dwyer M, Chambers SP, Markland W, Botfield M, Raybuck SA
Title Active-site residues of Escherichia coli DNA gyrase required in coupling ATP hydrolysis to DNA supercoiling and amino acid substitutions leading to novobiocin resistance.
Related PDB
Related UniProtKB

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.

Created Updated
2004-04-25 2009-02-26