HAMAP logo

HAMAP rule MF_01898

Send feedback

General rule information [?]

Accession MF_01898
Dates 18-MAY-2011 (Created)
15-JUN-2023 (Last updated, Version 17)
Name GyrB
Scope(s) Bacteria
Template(s) P0AES6 (GYRB_ECOLI); P9WG45 (GYRB_MYCTU); P0A2I3 (GYRB_SALTY); O67137 (TOP4B_AQUAE); [ Recover all ]
Triggered by HAMAP; MF_01898 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier GYRB
Protein name RecName: Full=DNA gyrase subunit B;
Gene name Name=gyrB;

Comments [?]

FUNCTIONA type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.
CATALYTIC ACTIVITY Reaction=ATP-dependent breakage, passage and rejoining of double- stranded DNA.; EC=;
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+).
SUBUNITHeterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.
MISCELLANEOUSFew gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.
SIMILARITYBelongs to the type II topoisomerase GyrB family.

Keywords [?]

Gene Ontology [?]

GO:0005524; Molecular function:ATP binding
GO:0003918; Molecular function:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0006261; Biological process:DNA-templated DNA replication
GO:0006265; Biological process:DNA topological change
GO:0005737; Cellular component:cytoplasm

Cross-references [?]

Pfam PF00204; DNA_gyraseB; 1;
Pfam PF00986; DNA_gyraseB_C; 1;
Pfam PF02518; HATPase_c; 1;
Pfam PF01751; Toprim; 0-1;
NCBIfam TIGR01059; GyrB; 1;

Features [?]

Key From To Description Tag Condition FTGroup
BINDING 424 424 /ligand="Mg(2+)"
BINDING 498 498 /ligand="Mg(2+)"
BINDING 498 498 /ligand="Mg(2+)"
BINDING 500 500 /ligand="Mg(2+)"
SITE 449 449 /note="Interaction with DNA" K
SITE 452 452 /note="Interaction with DNA" N

Additional information [?]

Size range 632-815 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments The degree of DNA negative supercoiling has been studied in very few bacteria, E.coli gyrase is extra efficient compared to other bacteria. The enzyme from Aquifex aeolicus does not have the ability to negatively supercoil DNA as its GyrA subunit has lost the GyrA-box. Some Cyanobacteriota contain inteins.

View rule in raw text format (no links)