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PDBsum entry 1epo
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Hydrolase/hydrolase inhibitor
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PDB id
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1epo
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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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Direct observation by X-Ray analysis of the tetrahedral "intermediate" of aspartic proteinases.
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Authors
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B.Veerapandian,
J.B.Cooper,
A.Sali,
T.L.Blundell,
R.L.Rosati,
B.W.Dominy,
D.B.Damon,
D.J.Hoover.
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Ref.
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Protein Sci, 1992,
1,
322-328.
[DOI no: ]
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PubMed id
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Abstract
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We report the X-ray analysis at 2.0 A resolution for crystals of the aspartic
proteinase endothiapepsin (EC 3.4.23.6) complexed with a potent
difluorostatone-containing tripeptide renin inhibitor (CP-81,282). The scissile
bond surrogate, an electrophilic ketone, is hydrated in the complex. The pro-(R)
(statine-like) hydroxyl of the tetrahedral carbonyl hydrate is hydrogen-bonded
to both active-site aspartates 32 and 215 in the position occupied by a water in
the native enzyme. The second hydroxyl oxygen of the hydrate is hydrogen-bonded
only to the outer oxygen of Asp 32. These experimental data provide a basis for
a model of the tetrahedral intermediate in aspartic proteinase-mediated cleavage
of the amide bond. This indicates a mechanism in which Asp 32 is the proton
donor and Asp 215 carboxylate polarizes a bound water for nucleophilic attack.
The mechanism involves a carboxylate (Asp 32) that is stabilized by extensive
hydrogen bonding, rather than an oxyanion derivative of the peptide as in serine
proteinase catalysis.
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Figure 3.
Fig. 3. Thestereochemistryandinteractionsofthetetrahedralhydratewiththeenzyme.Interatomicdistancesaretakenfrom
therefinedStructure, hasanestimatedcoordinateerrorof 0.2 A. Theinputfor aGaussian 88 calculationwascreated
from heX-raypositionsforthecarboxygroupsofAsp 2 and 215, and, from thestatineresidue,thetwohydroxyloxygens,
thetwofluorines,andthetwocarbonstheyareattachedto.Hydrogenatomswerethenaddedusingstandardbondlengthsand
anglestoformtwopossiblecomplexes(theoneshown,andanalternativearrangement in whichAsp 2 is protonatedandAp
215 charged).
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Figure 4.
Fig. 4. proposed mechanism for proteolytic cleavage of the amide
bond by an aspartic proteinase.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1992,
1,
322-328)
copyright 1992.
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Secondary reference #1
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Title
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A structural comparison of 21 inhibitor complexes of the aspartic proteinase from endothia parasitica.
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Authors
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D.Bailey,
J.B.Cooper.
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Ref.
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Protein Sci, 1994,
3,
2129-2143.
[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
perfect match.
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Figure 3.
Fig. 3. hydrogen bondinteractions with inhibitorsare shown (top) with agraph showing te donor-acceptor dis-
tances for the 21 nhibitor complexes (+ indicates an 0. . .H-N interaction, @ indicates an 0. . .H-N nteraction with an
at theproton greater than 160'. and X indicates n 0. . .H-0 interaction). Some of theiteractions with the aspartate carbox-
yls willbe van er Waals contactsratherthan hydrogen bonds (see text for discussion of proton locations).
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Figure 5.
Fig. 5. A: distribution of x, angles observed for each position of the inhibitors. The distribution of x2 angles.
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The above figures are
reproduced from the cited reference
with permission from the Protein Society
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Secondary reference #2
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Title
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X-Ray analyses of aspartic proteinases. The three-Dimensional structure at 2.1 a resolution of endothiapepsin.
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Authors
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T.L.Blundell,
J.A.Jenkins,
B.T.Sewell,
L.H.Pearl,
J.B.Cooper,
I.J.Tickle,
B.Veerapandian,
S.P.Wood.
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Ref.
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J Mol Biol, 1990,
211,
919-941.
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PubMed id
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