 |
PDBsum entry 1i32
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1i32
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Conformational changes in leishmania mexicana glyceraldehyde-3-Phosphate dehydrogenase induced by designed inhibitors.
|
|
|
Authors
|
|
S.Suresh,
J.C.Bressi,
K.J.Kennedy,
C.L.Verlinde,
M.H.Gelb,
W.G.Hol.
|
|
|
Ref.
|
|
J Mol Biol, 2001,
309,
423-435.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The glycolytic enzymes of trypanosomes are attractive drug targets, since the
blood-stream form of Trypanosoma brucei lacks a functional citric acid cycle and
is dependent solely on glycolysis for its energy requirements.
Glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from the pathogenic
trypanosomatids T. brucei, Trypanosoma cruzi and Leishmania mexicana are quite
similar to each other, and yet have sufficient structural differences compared
to the human enzyme to enable the structure-based design of compounds that
selectively inhibit all three trypanosomatid enzymes but not the human
homologue.Adenosine analogs with substitutions on N-6 of the adenine ring and on
the 2' position of the ribose moiety were designed, synthesized and tested for
inhibition. Two crystal structures of L. mexicana glyceraldehyde-3-phosphate
dehydrogenase in complex with high-affinity inhibitors that also block parasite
growth were solved at a resolution of 2.6 A and 3.0 A. The complexes
crystallized in the same crystal form, with one and a half tetramers in the
crystallographic asymmetric unit. There is clear electron density for the
inhibitor in all six copies of the binding site in each of the two structures.
The L. mexicana GAPDH subunit exhibits substantial structural plasticity upon
binding the inhibitor. Movements of the protein backbone, in response to
inhibitor binding, enlarge a cavity at the binding site to accommodate the
inhibitor in a classic example of induced fit. The extensive hydrophobic
interactions between the protein and the two substituents on the adenine
scaffold of the inhibitor provide a plausible explanation for the high affinity
of these inhibitors for trypanosomatid GAPDHs.
|
|
|
|
|
|
|
|
Figure 2.
Figure 2.
(a) Model-unbiased 6-fold averaged 2F
o
-
F
c
map of NMDBA bound to L. mexicana GAPDH at 2.6 A
Ê
con-
toured at 0.82s to within 2.0 A
Ê
of NMDBA atoms. The map was calculated after refining the six protein monomers
in the asymmetric unit and prior to modeling in the bound inhibitor (NMDBA, gold C atoms). In (a)-(d) residues in
green and violet are from adjacent monomers of the biological tetramer. (b) Model-unbiased sixfold averaged 2F
o
-
F
c
map of TNDBA bound to L. mexicana GAPDH at 3.0 A
Ê
, contoured at 0.82s to within 2.0 A
Ê
of TNDBA atoms.
(a) and (b) were made with Bobscript.
41
(c) Superposition of the six copies of the bound inhibitor NMDBA (gold C
atoms), in the crystal structure in complex with L. mexicana GAPDH. The 358 C
a
atoms of each monomer were used
in the superposition. (d) Superposition of the crystal structures of L. mexicana GAPDH in complex with NMDBA
(gold) and the structure in complex with TNDBA (grey). (c) and (d) Created with MOLSCRIPT
38
and Raster3D.
39,40
|
|
Figure 3.
Figure 3. (a) Schematic drawn by LIGPLOT
42
showing interactions of NMDBA with L. mexicana GAPDH. (b) Sche-
matic drawn by LIGPLOT
42
showing interactions of TNDBA with L. mexicana GAPDH.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
309,
423-435)
copyright 2001.
|
|
|
|
|
|
|
