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Overview for MACiE Entry M0064

Version history

General Information

EC Number: 5.99.1.2 (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
C00271
CHEBI:9160
single-stranded DNA
C00271
CHEBI:9160

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.

View similar reactions (composite manual annotation)


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

References

  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
Similarity
M0232 DNA topoisomerase (type IB) 1a41 0.3461 0.5142 Compare

Compare of the other reactions in MACiE with EC number 5.99.1.2


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

GOA logo
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)
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