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HAMAP rule MF_01898

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General rule information [?]

Accession	MF_01898
Dates	18-MAY-2011 (Created) 15-JUN-2023 (Last updated, Version 17)
Name	GyrB
Scope(s)	Bacteria Archaea
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; EC=5.6.2.2;
Gene name	Name=gyrB;

Comments [?]

FUNCTION	A 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=5.6.2.2;
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+).
SUBUNIT	Heterotetramer, 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.
SUBCELLULAR LOCATION	Cytoplasm.
MISCELLANEOUS	Few 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.
SIMILARITY	Belongs 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 [?]

PROSITE	PS00177; TOPOISOMERASE_II; 1;
Pfam	PF00204; DNA_gyraseB; 1;
Pfam	PF00986; DNA_gyraseB_C; 1;
Pfam	PF02518; HATPase_c; 1;
Pfam	PF01751; Toprim; 0-1;
PRINTS	PR00418; TPI2FAMILY; 1;
PROSITE	PS50880; TOPRIM; 1;
NCBIfam	TIGR01059; GyrB; 1;

Features [?]

From: GYRB_ECOLI (P0AES6)

Key

From

Description

Tag

Condition

FTGroup

BINDING

424

/ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"
/ligand_note="catalytic"

BINDING

498

/ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"
/ligand_note="catalytic"

BINDING

498

/ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"

BINDING

500

/ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"

SITE

449

/note="Interaction with DNA"

SITE

452

/note="Interaction with DNA"

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.

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