2GCI

The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an asparte/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1145-1161

  • DOI: 10.1016/j.jmb.2007.01.062
  • Primary Citation of Related Structures:  
  • Also Cited By: 2YIM

  • PubMed Abstract: 
  • Alpha-methylacyl-CoA racemases are essential enzymes for branched-chain fatty acid metabolism. Their reaction mechanism and the structural basis of their wide substrate specificity are poorly understood. High-resolution crystal structures of Mycobact ...

    Alpha-methylacyl-CoA racemases are essential enzymes for branched-chain fatty acid metabolism. Their reaction mechanism and the structural basis of their wide substrate specificity are poorly understood. High-resolution crystal structures of Mycobacterium tuberculosis alpha-methylacyl-CoA racemase (MCR) complexed with substrate molecules show the active site geometry required for catalysis of the interconversion of (2S) and (2R)-methylacyl-CoA. The thioester oxygen atom and the 2-methyl group are in a cis-conformation with respect to each other. The thioester oxygen atom fits into an oxyanion hole and the 2-methyl group points into a hydrophobic pocket. The active site geometry agrees with a 1,1-proton transfer mechanism in which the acid/base-pair residues are His126 and Asp156. The structures of the complexes indicate that the acyl chains of the S-substrate and the R-substrate bind in an S-pocket and an R-pocket, respectively. A unique feature of MCR is a large number of methionine residues in the acyl binding region, located between the S-pocket and the R-pocket. It appears that the (S) to (R) interconversion of the 2-methylacyl chiral center is coupled to a movement of the acyl group over this hydrophobic, methionine-rich surface, when moving from its S-pocket to its R-pocket, whereas the 2-methyl moiety and the CoA group remain fixed in their respective pockets.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
probable alpha-methylacyl-CoA racemase MCR
A, B, C, D
360Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: mcr
Find proteins for O06543 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O06543
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MRR
Query on MRR

Download SDF File 
Download CCD File 
A, B, C, D
(R)-2-METHYLMYRISTOYL-COENZYME A
[5-(6-AMINOPURIN-9-YL)-2-[[[[3-[2-(2-(R)-2-METHYLTETRADECANOYL)-SULFANYLETHYLCARBAMOYL ETHYLCARBAMOYL]-3-HYDROXY-2,2-DIMETHYL-PROPOXY]-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXYMETHYL]-4-HYDROXY-OXOLAN-3-YL]OXYPHOSPHONIC ACID
C36 H64 N7 O17 P3 S
KJEFZXSIQKASDI-MOTPQXBDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 180.700α = 90.00
b = 79.810β = 89.93
c = 118.060γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Data collection, Refinement description