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PDBsum entry 1fq7
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Hydrolase/hydrolase inhibitor
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PDB id
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1fq7
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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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X-Ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-Site specificity.
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Authors
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N.B.Cronin,
M.O.Badasso,
I.J tickle,
T.Dreyer,
D.J.Hoover,
R.L.Rosati,
C.C.Humblet,
E.A.Lunney,
J.B.Cooper.
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Ref.
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J Mol Biol, 2000,
303,
745-760.
[DOI no: ]
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PubMed id
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Abstract
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Saccharopepsin is a vacuolar aspartic proteinase involved in activation of a
number of hydrolases. The enzyme has great structural homology to mammalian
aspartic proteinases including human renin and we have used it as a model system
to study the binding of renin inhibitors by X-ray crystallography. Five
medium-to-high resolution structures of saccharopepsin complexed with
transition-state analogue renin inhibitors were determined. The structure of a
cyclic peptide inhibitor (PD-129,541) complexed with the proteinase was solved
to 2.5 A resolution. This inhibitor has low affinity for human renin yet binds
very tightly to the yeast proteinase (K(i)=4 nM). The high affinity of this
inhibitor can be attributed to its bulky cyclic moiety spanning P(2)-P(3)' and
other residues that appear to optimally fit the binding sub-sites of the enzyme.
Superposition of the saccharopepsin structure on that of renin showed that a
movement of the loop 286-301 relative to renin facilitates tighter binding of
this inhibitor to saccharopepsin. Our 2.8 A resolution structure of the complex
with CP-108,420 shows that its benzimidazole P(3 )replacement retains one of the
standard hydrogen bonds that normally involve the inhibitor's main-chain. This
suggests a non-peptide lead in overcoming the problem of susceptible peptide
bonds in the design of aspartic proteinase inhibitors. CP-72,647 which possesses
a basic histidine residue at P(2), has a high affinity for renin (K(i)=5 nM) but
proves to be a poor inhibitor for saccharopepsin (K(i)=3.7 microM). This may
stem from the fact that the histidine residue would not bind favourably with the
predominantly hydrophobic S(2) sub-site of saccharopepsin.
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Figure 5.
Figure 5. The charge distribution in the binding cavity of
saccharopepsin bound to inhibitor PD-129,541. The red negatively
charged "hot spot" indicates the position of the two catalytic
aspartate residues. Inhibitor residues P[4] and P[3]' are seen
emerging from the active site, while residues P[3] to P[2]' are
buried. Residues of helix h[N]2 (111 to 114) interact with P[3],
while residues of a hairpin structure (73 to 77) and the
polyproline loop (residues M289-I300) enclose the inhibitor.
This picture was prepared using GRASP [Nicholls et al 1993].
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Figure 6.
Figure 6. A superposition of the saccharopepsin/inhibitor
complexes: PD-129,541 (red); PD-133,450 (purple); CP-108,420
(aquamarine); CP-72,647 (green); CP-81,198 (blue) and CP-81,282
(grey). Their conformations are most conserved in the S[3] to
S[1]' sub-sites.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
303,
745-760)
copyright 2000.
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Secondary reference #1
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Title
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The three-Dimensional structure at 2.4 a resolution of glycosylated proteinase a from the lysosome-Like vacuole of saccharomyces cerevisiae.
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Authors
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C.F.Aguilar,
N.B.Cronin,
M.Badasso,
T.Dreyer,
M.P.Newman,
J.B.Cooper,
D.J.Hoover,
S.P.Wood,
M.S.Johnson,
T.L.Blundell.
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Ref.
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J Mol Biol, 1997,
267,
899-915.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. Electrostatic potential of proteinase A sampled at the molecular surface of the enzyme with a probe sphere
of radius 1.4 Å (blue, basic; red, acidic) generated using DELPHI (Sharp & Nicholls, 1990).
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Figure 7.
Figure 7. Interactions between enzyme and inhibitor; least squares superposition of the complex of yeast proteinase
A-CP-81,282 and the complex of endothiapepsin CP-81,282 (Veerapandian et al., 1992).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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