2YIM

The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue

Summary for 2YIM

• Entry DOI: 10.2210/pdb2yim/pdb
• Related: 1X74
• Descriptor: PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE ), GLYCEROL, 2-METHYLACETOACETYL COA, ... (5 entities in total)
• Functional Keywords: isomerase, methyl-coa racemase, transition state, molecular dynamics, qm/mm, oxyanion hole
• Biological source: MYCOBACTERIUM TUBERCULOSIS
• Total number of polymer chains: 4
• Total formula weight: 159000.12

Authors

Sharma, S.,Bhaumik, P.,Venkatesan, R.,Hiltunen, J.K.,Conzelmann, E.,Juffer, A.H.,Wierenga, R.K. (deposition date: 2011-05-16, release date: 2012-03-28, Last modification date: 2023-12-20)

Primary citation

Sharma, S.,Bhaumik, P.,Schmitz, W.,Venkatesan, R.,Hiltunen, J.K.,Conzelmann, E.,Juffer, A.H.,Wierenga, R.K.
The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed Qm/Mm Calculations.
J Phys Chem B, 116:3619-, 2012

PubMed Abstract: In the active site of the bacterial α-methylacyl-CoA racemase of Mycobacterium tuberculosis (MCR), the chirality of the 2-methyl branched C2-atom is interconverted between (S) and (R) isomers. Protein crystallographic data and quantum mechanics/molecular mechanics (QM/MM) computational approaches show that this interconversion is achieved via a planar enolate intermediate. The crystal structure, at 1.4 Å, visualizes the mode of binding of a reaction intermediate analogue, 2-methylacetoacetyl-CoA, in a well-defined planar enolate form. The computational studies confirm that in the conversion from (S) to (R), first a proton is abstracted by Nδ1 (His126), and subsequently the planar enolate form is reprotonated by Oδ2 (Asp156). The calculations also show that the negatively charged thioester oxygen of the enolate intermediate is stabilized by an oxyanion hole formed by N (Asp127), as well as by the side chain atoms of the catalytic residues, Asp156 and His126, both being protonated simultaneously, at the intermediate stage of the catalytic cycle. The computational analysis also reveals that the conversion of the (S)- to (R)- chirality is achieved by a movement of 1.7 Å of the chiral C2-carbon, with smaller shifts (approximately 1 Å) of the carbon atom of the 2-methyl group, the C3-atom of the fatty acid tail, and the C1-carbon and O1-oxygen atoms of the thioester moiety.

PubMed: 22360758
DOI: 10.1021/JP210185M

Experimental method

X-RAY DIFFRACTION (1.41 Å)