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Catalytic Site Atlas

CSA LITERATURE entry for 1ab4

E.C. nameDNA topoisomerase (ATP-hydrolysing)
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 5.99.1.3
CSA Homologues of 1ab4There are 12 Homologs
CSA Entries With UniProtID P0AES4
CSA Entries With EC Number 5.99.1.3
PDBe Entry 1ab4
PDBSum Entry 1ab4
MACiE Entry 1ab4

Literature Report

IntroductionE. coli DNA gyrase is a member of the family of type II topoisomerases, which change the topology of DNA by cleaving both the phosphodiester backbones of the double-stranded DNA, transporting another double-stranded segement through the enzyme bridged gap, and then religating the DNA.
Therefore, E. coli DNA gyrase catalyses the relaxation of negatively supercoiled DNA, and is uniquely also able to introduce negative supercoils into DNA at the expense of ATP hydrolysis.
By introducing a transient break into the DNA substrate, pasing another piece of DNA though the gap and releasing it, the enzyme relieves topological contraints caused by replication and transcription complexes moving along the DNA.
The enzyme consists of 2 GyrA and 2 GyrB subunits. The catalytic domain is found on the GyrA subunit, whilst the ATP hydrolysis site is found on GyrB.
MechansimThe DNA gyrase enzyme catalyses the cleavage of and religation of DNA.
1. The active site Tyr 122 is polarised by the magnesium ion, making it more susceptible to deprotonation by the his 78 general base of GyrA. 2. Tyr 122 nucleophilically attacks the scissile phosphate group, which forms a negatively charged pentacovalent phosphate intermediate. 3. This intermediate is stabilised by both magnesium ions and also by the positively charged side chain of Arg 32 on the GyrA subunit. 4. The 3' bridging O atom is stabilised by Mg2+ to make to 3' oxyanion a better leaving group and to ensure the 3'-hydroxyl group is produced. 5. The unstable 3'-oxyanion group is protonated by an unidentified acid (possibly conserved Lys 449 of GyrB).
Reaction

Catalytic Sites for 1ab4

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
TyrA122122macie:sideChainTyr 122 is deprotonated by the general base His 78, and is also polarised by a co-ordinated magnesium ion. This activates Tyr 122 to nucleophilic attack of the substrate scissile phosphate group.
ArgA3232macie:sideChainThe side chain of Arg 32 stabilises the transition state through hydrogen bonding.
HisA7878macie:sideChainThe His 78 acts as a general base, deprotonating the nucleophilic Tyr 122 residue.

Literature References

Notes:There are two Mg2+ ions, which are cofactors. One metal ion stabilises the pentacovalent phosphate transition state, as well as the 3'-oxyanion to make it a better leaving group. The other metal ion stabilises the negatively charged transition state, and polarises the attacking Tyr residue, so it is more prone to protonation.
Noble CG
The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism.
J Mol Biol 2002 318 361-371
PubMed: 12051843
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