PDBsum entry 1yps

Complex (aspartyl protease/peptide)

PDB id: 1yps

Contents

Protein chain

311 a.a.

Ligands

ARG-VAL-SER-MET-ILE-LYS-ASN-ARG-ARG

Theoretical model

PDB id:

1yps

Name:

Complex (aspartyl protease/peptide)

Title:

Molecular modeling of the aspartic protease yapsin 1

Structure:

Yapsin 1. Chain: a. Synonym: yap3p, yeast aspartic protease 3. Biological_unit: disulfide-linked heterodimer. Cck (18-26) peptide. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Cellular_location: periplasm. Gene: yps1. Synthetic: yes

Authors:

V.Olsen,K.Guruprasad,N.X.Cawley,H.-C.Chen,T.L.Blundell, Y.P.Loh

Key ref:

V.Olsen et al. (1998). 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. Biochemistry, 37, 2768-2777. PubMed id: 9485427 DOI: 10.1021/bi9724826

Date:

09-Apr-98 Release date: 17-Jun-98

Protein chain

P32329  (YPS1_YEAST) -  Aspartic proteinase 3

Seq: 569 a.a.

Struc: 311 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.23.- - ?????

DOI no: 10.1021/bi9724826

Biochemistry 37:2768-2777 (1998)

PubMed id: 9485427

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.

V.Olsen, K.Guruprasad, N.X.Cawley, H.C.Chen, T.L.Blundell, Y.P.Loh.

ABSTRACT

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.