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PDBsum entry 1a7k
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Oxidoreductase
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PDB id
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1a7k
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of leishmania mexicana glycosomal glyceraldehyde-3-Phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.
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Authors
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H.Kim,
W.G.Hol.
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Ref.
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J Mol Biol, 1998,
278,
5.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
96%.
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Abstract
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The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
from the trypanosomatid parasite Leishmania mexicana in a new crystal form has
been determined by X-ray crystallography. The protein crystallizes in space
group P21 with one 156 kDa tetramer per asymmetric unit. The model of the
protein with bound NAD+s and phosphates has been refined against 81% complete
data from 10.0 to 2. 8 A to a crystallographic Rfactor of 0.217. The present
structure confirms two key aspects of the previously reported orthorhombic
crystal structure of L. mexicana GAPDH (LmGAPDH): the unusual conformation of a
loop in the active site, and the repositioning of the inorganic phosphate
binding site compared with crystal structures of GAPDHs from other organisms. As
the monoclinic crystals of LmGAPDH were grown at a phosphate concentration and
pH that were even closer to physiological conditions than were the orthorhombic
LmGAPDH crystals, the present structure reinforces the physiological relevance
of the active site structure seen in the previous orthorhombic crystal of
LmGAPDH.
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Figure 2.
Figure 2. Stereoview of 220s
loop in monoclinic LmGAPDH.
(a) Simulated annealing omit
Fo
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Fc electron density map
(Hodel et al., 1992; Read, 1986) of
monoclinic LmGAPDH for which
Pro223 to Ala228 were omitted
from the Fc calculations. The map
contour level is 2.0s. Superimposed
on the electron density is the
refined conformation of the 220s
loop in monoclinic LmGAPDH.
(b) Superposition of monoclinic
and orthorhombic LmGAPDHs at
the 220s loop region. Monoclinic
LmGAPDH is drawn in thick
lightly shaded bonds. Orthorhom-
bic LmGAPDH is drawn in thin
filled bonds. This figure was made
with MOLSCRIPT.
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Figure 3.
Figure 3. Representative Rama-
chandran plot of the A subunit of
LmGAPDH in the monoclinic crys-
tal form. Glycine residues are indi-
cated with hollow circles, all other
residues with filled circles. The resi-
dues in the 220s loop, Pro223 to
Ala228 are labelled.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
278,
5-0)
copyright 1998.
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Secondary reference #1
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Title
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Crystal structure of glycosomal glyceraldehyde-3-Phosphate dehydrogenase from leishmania mexicana: implications for structure-Based drug design and a new position for the inorganic phosphate binding site.
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Authors
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H.Kim,
I.K.Feil,
C.L.Verlinde,
P.H.Petra,
W.G.Hol.
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Ref.
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Biochemistry, 1995,
34,
14975-14986.
[DOI no: ]
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PubMed id
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