 |
PDBsum entry 2gce
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
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.
|
|
|
Authors
|
|
P.Bhaumik,
W.Schmitz,
A.Hassinen,
J.K.Hiltunen,
E.Conzelmann,
R.K.Wierenga.
|
|
|
Ref.
|
|
J Mol Biol, 2007,
367,
1145-1161.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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 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.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. (a) The substrate molecules of mammalian Amacr. The
covalent structures of pristanoyl-CoA,
3,7,12-trihydroxycoprostanoyl-CoA and ibuprofenoyl-CoA are
shown. The methyl group attached to the chiral C^α atom is
referred to as the 2-methyl moiety. Amacr interconverts the
chirality of this C^α atom. (b) The covalent structures of the
substrate analogues acetyl-CoA and acetoacetyl-CoA. The
conformation of the acetoacetyl moiety shown at the left
concerns the conformation that allows for internal hydrogen
bonding. The rotamer at the right visualizes the observed mode
of binding in the structure of the acetoacetyl-CoA MCR complex.
(c) The reaction catalyzed by MCR. The catalytic interconversion
of the two enantiomers takes place in the enzyme active site by
a 1,1-proton transfer involving a catalytic acid/base-pair,
which in MCR is His126 (base B[1]) and Asp156 (base B[2]). In
the anionic intermediate, the C^α atom is planar and a negative
charge develops on the thioester oxygen atom.
|
|
Figure 9.
Figure 9. The reaction mechanism of the interconversion of
(2S)-methylacyl-CoA to (2R)-methylacyl-CoA by MCR, as suggested
from the crystal structure and kinetic data. In this enzymatic
conversion, His126 acts as a general base (abstracting a proton
from the α-carbon atom of the (S)-compound) and Asp156 acts
as a general acid (donating a proton to the α-carbon atom of
the (S)-compound). Dotted lines highlight important stabilizing
interactions. The oxyanion of the reaction intermediate is
stabilized by hydrogen bonding interactions with the main-chain
NH group of Asp127, as well as with the protonated side-chains
of His126 and Asp156.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
367,
1145-1161)
copyright 2007.
|
|
|
|
|
|
|
