Mechanism of mycolic acid cyclopropane synthase: a theoretical study.
The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden.
Rong-Zhen
RZ
Liao
Polina
P
Georgieva
Jian-Guo
JG
Yu
Fahmi
F
Himo
D001426:Bacterial Proteins / Q000378:metabolism*; D020134:Catalytic Domain; D003198:Computer Simulation; D008780:Methyltransferases / Q000737:chemistry / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D009171:Mycolic Acids / Q000378:metabolism*; D011487:Protein Conformation
D001426:Bacterial Proteins; D009171:Mycolic Acids; D008780:Methyltransferases; C019964:cyclopropane synthetase