DB code: M00137

CATH domain 3.90.199.10 : Topoisomerase II; domain 5 Catalytic domain
3.30.1360.40 : Gyrase A; domain 2
1.10.268.10 : Topoisomerase; domain 3
2.-.-.- :
E.C. 5.99.1.3
CSA 1ab4
M-CSA 1ab4
MACiE

CATH domain Related DB codes (homologues)
1.10.268.10 : Topoisomerase; domain 3 M00048
3.30.1360.40 : Gyrase A; domain 2 M00048
3.90.199.10 : Topoisomerase II; domain 5 M00048

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AES4 DNA gyrase subunit A
EC 5.99.1.3
NP_416734.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490470.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03989 (DNA_gyraseA_C)
PF00521 (DNA_topoisoIV)
[Graphical View]
Q9LCX6
Gyrase subunit A
PF03989 (DNA_gyraseA_C)
PF00521 (DNA_topoisoIV)
[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
P0AES4 GYRA_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.
Q9LCX6 Q9LCX6_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
1ab4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ab4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ab4A03 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.
Swiss-prot;P0AES4 & literature [19]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ab4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 32;HIS 78;TYR 122
1ab4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ab4A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[19]
Fig.9 1

References
[1]
Resource
Comments
Medline ID
PubMed ID 225107
Journal Cold Spring Harb Symp Quant Biol
Year 1979
Volume 43 Pt 1
Pages 35-40
Authors Gellert M, Mizuuchi K, O'Dea MH, Ohmori H, Tomizawa J
Title DNA gyrase and DNA supercoiling.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 225110
Journal Cold Spring Harb Symp Quant Biol
Year 1979
Volume 43 Pt 1
Pages 41-52
Authors Peebles CL, Higgins NP, Kreuzer KN, Morrison A, Brown PO, Sugino A, Cozzarelli NR
Title Structure and activities of Escherichia coli DNA gyrase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2153834
Journal J Mol Biol
Year 1990
Volume 211
Pages 211-20
Authors Krueger S, Zaccai G, Wlodawer A, Langowski J, O'Dea M, Maxwell A, Gellert M
Title Neutron and light-scattering studies of DNA gyrase and its complex with DNA.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2172550
Journal J Mol Biol
Year 1990
Volume 215
Pages 493-5
Authors Reece RJ, Dauter Z, Wilson KS, Maxwell A, Wigley DB
Title Preliminary crystallographic analysis of the breakage-reunion domain of the Escherichia coli DNA gyrase A protein.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1327123
Journal Biochemistry
Year 1992
Volume 31
Pages 9642-6
Authors Cullis PM, Maxwell A, Weiner DP
Title Energy coupling in DNA gyrase: a thermodynamic limit to the extent of DNA supercoiling.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8538787
Journal Nature
Year 1996
Volume 379
Pages 225-32
Authors Berger JM, Gamblin SJ, Harrison SC, Wang JC
Title Structure and mechanism of DNA topoisomerase II.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522
Medline ID 97422287
PubMed ID 9278055
Journal Nature
Year 1997
Volume 388
Pages 903-6
Authors Morais Cabral JH, Jackson AP, Smith CV, Shikotra N, Maxwell A, Liddington RC
Title Crystal structure of the breakage-reunion domain of DNA gyrase.
Related PDB 1ab4
Related UniProtKB P0AES4
[8]
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
[9]
Resource
Comments
Medline ID
PubMed ID 9685374
Journal J Biol Chem
Year 1998
Volume 273
Pages 20252-60
Authors Liu Q, Wang JC
Title Identification of active site residues in the "GyrA" half of yeast DNA topoisomerase II.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9437427
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 31-6
Authors Klabunde T, Sharma S, Telenti A, Jacobs WR Jr, Sacchettini JC
Title Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10521257
Journal Biochemistry
Year 1999
Volume 38
Pages 13502-11
Authors Williams NL, Maxwell A
Title Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10571989
Journal Biochemistry
Year 1999
Volume 38
Pages 14157-64
Authors Williams NL, Maxwell A
Title Locking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10356321
Journal J Mol Biol
Year 1999
Volume 289
Pages 447-58
Authors Ashizawa Y, Yokochi T, Ogata Y, Shobuike Y, Kato J, Ikeda H
Title Mechanism of DNA gyrase-mediated illegitimate recombination: characterization of Escherichia coli gyrA mutations that confer hyper-recombination phenotype.
Related PDB
Related UniProtKB
[14]
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
[15]
Resource
Comments
Medline ID
PubMed ID 10411889
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 8414-9
Authors Kampranis SC, Bates AD, Maxwell A
Title A model for the mechanism of strand passage by DNA gyrase.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11451702
Journal Antimicrob Agents Chemother
Year 2001
Volume 45
Pages 2378-80
Authors Friedman SM, Lu T, Drlica K
Title Mutation in the DNA gyrase A Gene of Escherichia coli that expands the quinolone resistance-determining region.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11408229
Journal Antimicrob Agents Chemother
Year 2001
Volume 45
Pages 2098-105
Authors Maurin M, Abergel C, Raoult D
Title DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11469868
Journal J Mol Biol
Year 2001
Volume 311
Pages 195-203
Authors Sissi C, Perdona E, Domenici E, Feriani A, Howells AJ, Maxwell A, Palumbo M
Title Ciprofloxacin affects conformational equilibria of DNA gyrase A in the presence of magnesium ions.
Related PDB
Related UniProtKB
[19]
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

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.

Created Updated
2004-04-23 2009-02-26