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HAMAP rule MF_00953

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General rule information [?]

Accession MF_00953
Dates 27-MAR-2013 (Created)
26-JAN-2023 (Last updated, Version 12)
Name Topoisom_3_prok
Scope
Bacteria
Template P14294 (TOP3_ECOLI)
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
TOP3
Protein name
RecName: Full=DNA topoisomerase 3;
EC 5.6.2.1;
AltName: Full=DNA topoisomerase III;
Gene name
topB

Comments [?]

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 Mg(2+)
Note: Binds two Mg(2+) per subunit.
else case <FTGroup:2>
Cofactor Mg(2+)
end case
Similarity Belongs to the type IA topoisomerase family.

Keywords [?]

DNA-binding
Isomerase
case <FTGroup:1> or <FTGroup:2>
Magnesium
Metal-binding
end case
Topoisomerase

Gene Ontology [?]

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 [?]

PROSITE PS00396; TOPOISOMERASE_I_PROK; 1;
PS50880; TOPRIM; 1; trigger=PRU00995;
Pfam PF01131; Topoisom_bac; 1;
PF01751; Toprim; 1;
PRINTS PR00417; PRTPISMRASEI; 1;
TIGRFAMs TIGR01056; topB; 1;

Features [?]

From: TOP3_ECOLI (P14294)
Key     From     To       Description   Tag   Condition   FTGroup
REGION (Optional)     194     199       Interaction with DNA     [SN]-x-G-R-V-Q  
ACT_SITE     328     328       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 (Optional)     61     61       Interaction with DNA     W  
SITE (Optional)     170     170       Interaction with DNA     W  
SITE (Optional)     178     178       Interaction with DNA     R  
SITE (Optional)     185     185       Interaction with DNA     R  
SITE (Optional)     330     330       Interaction with DNA     R  

Additional information [?]

Size range 610-765 amino acids
Related rules None
Fusion None


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