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PDBsum entry 1yps
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Complex (aspartyl protease/peptide)
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PDB id
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1yps
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References listed in PDB file
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Key reference
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Title
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Cleavage efficiency of the novel aspartic protease yapsin 1 (yap3p) enhanced for substrates with arginine residues flanking the p1 site: correlation with electronegative active-Site pockets predicted by molecular modeling.
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Authors
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V.Olsen,
K.Guruprasad,
N.X.Cawley,
H.C.Chen,
T.L.Blundell,
Y.P.Loh.
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Ref.
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Biochemistry, 1998,
37,
2768-2777.
[DOI no: ]
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PubMed id
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Abstract
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Yapsin 1, a novel aspartic protease with unique specificity for basic residues,
was shown to cleave CCK13-33 at Lys23. Molecular modeling of yapsin 1 identified
the active-site cleft to have negative residues close to or within the S6, S3,
S2, S1, S1', S2', and S3' pockets and is more electronegative than
rhizopuspepsin or endothiapepsin. In particular, the S2' subsite has three
negative charges in and close to this pocket that can provide strong
electrostatic interactions with a basic residue. The model, therefore, predicts
that substrates with a basic residue in the P1 position would be favored with
additional basic residues binding to the other electronegative pockets. A
deletion of six residues close to the S1 pocket in yapsin 1, relative to
rhizopuspepsin and other aspartic proteases of known 3D structure, is likely to
affect its specificity. The model was tested using CCK13-33 analogues. We report
that yapsin 1 preferentially cleaves a CCK13-33 substrate with a basic residue
in the P1 position since the substrates with Ala in P1 were not cleaved.
Furthermore, the cleavage efficiency of yapsin 1 was enhanced for CCK13-33
analogues with arginine residues flanking the P1 position. An alanine residue,
substituting for the arginine residue in the P6 position in CCK13-33, resulted
in a 50% reduction in the cleavage efficiency. Substitution with arginine
residues downstream of the cleavage site at the P2', P3', or P6' position
increased the cleavage efficiency by 21-, 3- and 7-fold, respectively.
Substitution of Lys23 in CCK13-33 with arginine resulted not only in cleavage
after the substituted arginine residue, but also forced a cleavage after Met25,
suggesting that an arginine residue in the S2' pocket is so favorable that it
can affect the primary specificity of yapsin 1. These results are consistent
with the predictions from the molecular model of yapsin 1.
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