HAMAP rule MF_00953
General rule information
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| Accession | MF_00953 |
| Dates | 27-MAR-2013 (Created)
6-OCT-2023 (Last updated, Version 14) |
| Name | Topoisom_3_prok |
| Scope(s) |
Bacteria |
| Template(s) | P14294 (TOP3_ECOLI); [ Recover all ] |
| Triggered by |
HAMAP; MF_00953 (Get profile general information and statistics) |
Propagated annotation
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Identifier, protein and gene names
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| Identifier | TOP3 |
| Protein name | RecName: Full=DNA topoisomerase 3; EC=5.6.2.1; AltName: Full=DNA topoisomerase III; |
| Gene name | Name=topB; |
Comments
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| FUNCTION | Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA- (5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. |
| CATALYTIC ACTIVITY | Reaction=ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.; EC=5.6.2.1; |
| case <FTGroup:1> | |
| COFACTOR | Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Note=Binds two Mg(2+) per subunit.; |
| else case <FTGroup:2> | |
| COFACTOR | Name=Mg(2+); Xref=ChEBI:CHEBI:18420; |
| end case | |
| SIMILARITY | Belongs to the type IA topoisomerase family. |
Keywords
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| DNA-binding | |
| Isomerase | |
| case <FTGroup:1> or <FTGroup:2> | |
| Magnesium | |
| Metal-binding | |
| end case | |
| Topoisomerase | |
Gene Ontology
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| GO:0003917; Molecular function:DNA topoisomerase type I (single strand cut, ATP-independent) activity | |
| case <FTGroup:1> or <FTGroup:2> | |
| GO:0000287; Molecular function:magnesium ion binding | |
| end case | |
| GO:0006265; Biological process:DNA topological change | |
Cross-references
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| PROSITE | PS00396; TOPO_IA_1; 1; |
| PROSITE | PS52039; TOPO_IA_2; 1; |
| PROSITE | PS50880; TOPRIM; 1; |
| Pfam | PF01131; Topoisom_bac; 1; |
| Pfam | PF01751; Toprim; 1; |
| PRINTS | PR00417; PRTPISMRASEI; 1; |
| NCBIfam | TIGR01056; topB; 1; |
Features
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| From: TOP3_ECOLI (P14294) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| REGION | 194 | 199 | /note="Interaction with DNA" | [SN]-x-G-R-V-Q | ||||||||
| ACT_SITE | 328 | 328 | /note="O-(5'-phospho-DNA)-tyrosine intermediate" | Y | ||||||||
| case <OC:Pseudomonadota> | ||||||||||||
| BINDING | 7 | 7 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic" |
E | 1 | |||||||
| BINDING | 103 | 103 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" /ligand_note="catalytic" |
D | 1 | |||||||
| BINDING | 103 | 103 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
D | 1 | |||||||
| BINDING | 105 | 105 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
D | 1 | |||||||
| else | ||||||||||||
| BINDING | 7 | 7 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic" |
E | 2 | |||||||
| BINDING | 103 | 103 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic" |
D | 2 | |||||||
| end case | ||||||||||||
| SITE | 61 | 61 | /note="Interaction with DNA" | W | ||||||||
| SITE | 170 | 170 | /note="Interaction with DNA" | W | ||||||||
| SITE | 178 | 178 | /note="Interaction with DNA" | R | ||||||||
| SITE | 185 | 185 | /note="Interaction with DNA" | R | ||||||||
| SITE | 330 | 330 | /note="Interaction with DNA" | R | ||||||||
Additional information
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| Size range | 610-765 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |