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Catalytic Site Atlas

CSA LITERATURE entry for 1d6m

E.C. nameDNA topoisomerase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 5.99.1.2
CSA Homologues of 1d6m1i7d,1lmu,2o19,2o54,2o59,2o5c,2o5e,
CSA Entries With UniProtID P14294
CSA Entries With EC Number 5.99.1.2
PDBe Entry 1d6m
PDBSum Entry 1d6m
MACiE Entry M0064

Literature Report

IntroductionTopoisomerases catalyse the winding and unwinding of super-coiled DNA, a process vital during DNA replication, transcription and repair. Type I topoisomerases reversibly cut one strand of the DNA helix, and can only relax supercoils. Analysis of sequence and mutagenesis data indicates that the type Ia topoisomerases (those found in prokaryotes, and the example given here) may be related to the major family of type II topoisomerases (found in all life apart from some archaea). Type II topoisomerases cut both strands and can either relax or tighten super-coils, but require ATP hydrolysis for catalytic turnover. All topoisomerases recorded form an intermediate with a tyr-DNA covalent bond during catalysis.
MechansimThe Tyr328 acts as a nucleophile towards the phosphorous of the DNA molecule, forming a pentavalent transition state before eliminating the 5' DNA with concomitant deprotonation of Glu7. The DNA uncoils before Glu7 can deprotonate the 5'-OH, which initiates a nucleophilic attack upon the phosphorous atom. This again proceeds through a pentavalent transition state before eliminating Tyr328 and restoring the enzyme active site. The reaction requires Mg(II), which is bound by acidic glutamine residues. The metal's importance is shown by the detrimental effect to binding and activity brought about by mutation at these sites, however the role of the Mg as either structurally or catalytically essential is still uncertain.

Catalytic Sites for 1d6m

Literature References

Notes:
Changela A
Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule.
Nature 2001 411 1077-1081
PubMed: 11429611
Chen SJ
Identification of active site residues in Escherichia coli DNA topoisomerase I.
J Biol Chem 1998 273 6050-6056
PubMed: 9497321
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