Binding diversity of a noncovalent-type low-molecular-weight serine protease inhibitor and function of a catalytic water molecule: X-ray crystal structure of PKSI-527--inhibited trypsin.
PKSI-527 is a noncovalent-type low-molecular-weight inhibitor. The X-ray crystal structure of the trypsin-PKSI-527 complex revealed a binding mode (Form II) different from the previously reported one (Form I) [Nakamura, M. et al. (1995) Biochem. Biophys. Res. Commun. 213, 583--587]. In contrast to the previous case, the electron density of the inhibitor revealed the whole structure clearly. Each structural part of the inhibitor in Forms I and II was differently located at the active site, although the modes of binding of the terminal amino group to the Asp189 carboxyl group were similar. This binding diversity, which is a characteristic of the noncovalent-type low-molecular-weight inhibitor, provides a suitable example for estimating the possible mechanism toward the enzymatic inhibition, together with the structural basis necessary for a specific inhibitor. The mode of binding in Form II reflects the inhibitor-specific situation and is in contrast with the substrate-mimetic binding mode for Form I. Based on the generally accepted catalytic mechanism for serine protease, we propose that a water molecule located at the catalytic site plays an important role in blocking the catalytic function of the reactive Ser193 OH group.
Osaka University of Pharmaceutical Sciences, Nasahara, Takatsuki, Osaka 569-1094, Japan. tomoo@oysun01.oups.ac.jp
K
K
Tomoo
K
K
Satoh
Y
Y
Tsuda
K
K
Wanaka
S
S
Okamoto
A
A
Hijikata-Okunomiya
Y
Y
Okada
T
T
Ishida
D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D002417:Cattle; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008970:Molecular Weight; D010649:Phenylalanine / Q000031:analogs & derivatives / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D015842:Serine Proteinase Inhibitors / Q000737:chemistry* / Q000378:metabolism*; D014148:Tranexamic Acid / Q000031:analogs & derivatives / Q000737:chemistry* / Q000378:metabolism*; D014357:Trypsin / Q000737:chemistry* / Q000378:metabolism*; D014867:Water / Q000737:chemistry / Q000378:metabolism*
D015842:Serine Proteinase Inhibitors; D014867:Water; C064866:PKSI 527; D010649:Phenylalanine; D014148:Tranexamic Acid; D014357:Trypsin