HAMAP rule MF_01898
General rule information
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| Accession | MF_01898 |
| Dates | 18-MAY-2011 (Created) 15-JUN-2023 (Last updated, Version 17) |
| Name | GyrB |
| Scope | Bacteria
Archaea |
| Templates | P0AES6 (GYRB_ECOLI); P9WG45 (GYRB_MYCTU); P0A2I3 (GYRB_SALTY); O67137 (TOP4B_AQUAE): [Recover all] |
| Triggered by |
Propagated annotation
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Identifier, protein and gene names
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| Identifier |
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| Protein name |
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| Gene name |
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Comments
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| 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 | Mg(2+) Mn(2+) Ca(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
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Gene Ontology
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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.
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
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| PROSITE | PS00177; TOPOISOMERASE_II; 1; |
| Pfam | PF00204; DNA_gyraseB; 1; |
| PF00986; DNA_gyraseB_C; 1; | |
| PF02518; HATPase_c; 1; | |
| PF01751; Toprim; 0-1; | |
| PRINTS | PR00418; TPI2FAMILY; 1; |
| PROSITE | PS50880; TOPRIM; 1; trigger=PRU00995; |
| NCBIfam | TIGR01059; GyrB; 1; |
Features
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| From: GYRB_ECOLI (P0AES6) | ||||||||||||
| 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
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| 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. |