Crystal structure of aspartic proteinase from Irpex lacteus in complex with inhibitor pepstatin.
The crystal structure of Irpex lacteus aspartic proteinase (ILAP) in complex with pepstatin (a six amino acid residue peptide-like inhibitor) was determined at 1.3A resolution. ILAP is a pepsin-like enzyme, widely distributed in nature, with high milk-clotting activity relative to proteolytic activity. The overall structure was in good topological agreement with pepsin and other aspartic proteases. The structure and interaction pattern around the catalytic site were conserved, in agreement with the other aspartic proteinase/inhibitor complex structures reported previously. The high-resolution data also supported the transition state model, as proposed previously for the catalytic mechanism of aspartic proteinase. Unlike the other aspartic proteinases, ILAP was found to require hydrophobic residues either in the P(1) or P(1') site, and also in the P(4) and/or P(3) site(s) for secondary interactions. The inhibitor complex structure also revealed the substrate binding mechanism of ILAP at the P(3) and P(4) site of the substrate, where the inserted loop built up the unique hydrophobic pocket at the P(4) site.
Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. zui@affrc.go.jp
Zui
Z
Fujimoto
Yoshifumi
Y
Fujii
Satoshi
S
Kaneko
Hideyuki
H
Kobayashi
Hiroshi
H
Mizuno
D000595:Amino Acid Sequence; D000818:Animals; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001487:Basidiomycota / Q000201:enzymology*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010436:Pepstatins / Q000737:chemistry / Q000378:metabolism*; D011480:Protease Inhibitors / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D011522:Protons; D016415:Sequence Alignment; D013379:Substrate Specificity; D013552:Swine
D005656:Fungal Proteins; D010436:Pepstatins; D011480:Protease Inhibitors; D011522:Protons; D016282:Aspartic Acid Endopeptidases; C076494:aspartic proteinase, Irpex lacteus; C031375:pepstatin