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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
Templates P0AES6 (GYRB_ECOLI); P9WG45 (GYRB_MYCTU); P0A2I3 (GYRB_SALTY); O67137 (TOP4B_AQUAE): [Recover all]

Propagated annotation [?]

Identifier, protein and gene names [?]

Protein name
RecName: Full=DNA gyrase subunit B;
Gene name

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=;
Cofactor Mg(2+)
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 [?]

Pfam PF00204; DNA_gyraseB; 1;
PF00986; DNA_gyraseB_C; 1;
PF02518; HATPase_c; 1;
PF01751; Toprim; 0-1;
PROSITE PS50880; TOPRIM; 1; trigger=PRU00995;
NCBIfam TIGR01059; GyrB; 1;

Features [?]

Key     From     To       Description   Tag   Condition   FTGroup
BINDING     424     424       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic     E  
BINDING     498     498       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic     D  
BINDING     498     498       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2     D  
BINDING     500     500       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2     D  
SITE     449     449       Interaction with DNA     K  
SITE     452     452       Interaction with DNA     N  

Additional information [?]

Size range 632-815 amino acids
Related rules None
Fusion 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.