Overview for MACiE Entry M0064

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General Information

EC Number: (A member of the Isomerases, Other isomerases, Sole sub-subclass for isomerases that do not belong in the other subclasses)

Enzyme Name: DNA topoisomerase (type IA)

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1d6m - CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III (Resolution = 3.00 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of single-stranded DNA

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Image of single-stranded DNA

single-stranded DNA
single-stranded DNA

Overall Comment: Although Mg(II) is required for the relaxation of the supercoiled DNA, its role in catalysis is not yet determined [1].

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Stepwise Description of the Reaction

Step 1Tyr328 acts as a nucleophilic, attacking the phosphorous of the DNA molecule, which proceeds through a pentavalent transition state, before eliminating the 5' DNA, with concomitant deprotonation of Glu7.
Step 2The DNA uncoils before Glu7 deprotonates the 5'-OH, which initiates a nucleophilic attack upon the phosphorous atom, which proceeds through a pentavalent transition state, before eliminating Tyr328.

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Catalytic Residues Involved

Type Number Chain Location of Function
Glu 7 A Side Chain
Lys 8 A Side Chain
Tyr 328 A Side Chain
Arg 330 A Side Chain


  1. A. Changela et al. (2001), Nature, 411, 1077-1081. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule.
    Medline: 11429611
  2. J. J. Champoux (2002), Trends Pharmacol. Sci., 23, 199-201. A first view of the structure of a type IA topoisomerase with bound DNA.
    Medline: 12007989

Homologue information for M0064 (1d6m)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)

Entries with the same EC number (different mechanisms):

MACiE Entry Enzyme Name PDB code Composite
Reaction Similarity
Catalytic Machinery
M0232 DNA topoisomerase (type IB) 1a41 0.3461 0.5142 Compare

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Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

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nucleic acid binding (molecular function)
DNA binding (molecular function)
DNA topoisomerase activity (molecular function)
DNA topoisomerase type I activity (molecular function)
chromosome (cellular component)
DNA metabolic process (biological process)
DNA topological change (biological process)
DNA unwinding involved in DNA replication (biological process)