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HAMAP rule MF_00953

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General rule information [?]

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 [?]

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 Name=topB;

Comments [?]

FUNCTIONReleases 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
SIMILARITYBelongs 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; 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 [?]

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 [?]

Size range 610-765 amino acids
Related rules None
Fusion Nter: None Cter: None



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