2YIM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Literature

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.

Sharma, S.Bhaumik, P.Schmitz, W.Venkatesan, R.Hiltunen, J.K.Conzelmann, E.Juffer, A.H.Wierenga, R.K.

(2012) J Phys Chem B 116: 3619

  • DOI: 10.1021/jp210185m
  • Primary Citation of Related Structures:  
    2YIM

  • 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 ...

    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.


    Related Citations: 
    • The Catalysis of the 1,1-Proton Transfer by Alpha-Methyl-Acyl-Coa Racemase is Coupled to a Movement of the Fatty Acyl Moiety Over a Hydrophobic, Methionine-Rich Surface.
      Bhaumik, P., Schmitz, W., Hassinen, A., Hiltunen, J.K., Conzelmann, E., Wierenga, R.K.
      (2007) J Mol Biol 367: 1145

    Organizational Affiliation

    Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, Oulu, FI-90014, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )A, B, C, D360Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mcrRv1143
EC: 5.1.99.4
UniProt
Find proteins for O06543 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06543 
Go to UniProtKB:  O06543
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06543
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
MC4 Binding MOAD:  2YIM Kd: 1.20e+5 (nM) from 1 assay(s)
PDBBind:  2YIM Kd: 1.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.59α = 90
b = 80.17β = 91.41
c = 118.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Other