1MAY

BETA-TRYPSIN PHOSPHONATE INHIBITED

Summary for 1MAY

• Entry DOI: 10.2210/pdb1may/pdb
• Descriptor: BETA-TRYPSIN, CALCIUM ION, [N-(BENZYLOXYCARBONYL)AMINO](4-AMIDINOPHENYL)METHANE-PHOSPHONATE, ... (4 entities in total)
• Functional Keywords: hydrolase, serine protease, digestion, pancreas, zymogen, hydrolase (serine protease)
• Biological source: Bos taurus (cattle)
• Cellular location: Secreted, extracellular space: P00760
• Total number of polymer chains: 1
• Total formula weight: 23727.67

Authors

Bertrand, J.,Oleksyszyn, J.,Kam, C.,Boduszek, B.,Presnell, S.,Plaskon, R.,Suddath, F.,Powers, J.,Williams, L. (deposition date: 1996-02-06, release date: 1996-10-14, Last modification date: 2024-10-23)

Primary citation

Bertrand, J.A.,Oleksyszyn, J.,Kam, C.M.,Boduszek, B.,Presnell, S.,Plaskon, R.R.,Suddath, F.L.,Powers, J.C.,Williams, L.D.
Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models.
Biochemistry, 35:3147-3155, 1996

PubMed Abstract: X-ray structures of trypsin from bovine pancreas inactivated by diphenyl [N-(benzyloxycarbonyl)amino](4-amidinophenyl)methanephosphonate [Z-(4-AmPhGly)P(OPh)2] were determined at 113 and 293 K to 1.8 angstrom resolution and refined to R factors of 0.211 (113 K) and 0. 178 (293 K). The structures reveal a tetrahedral phosphorus covalently bonded to the O gamma of the active site serine. Covalent bond formation is accompanied by the loss of both phenoxy groups. The D-stereoisomer of Z-(4-AmPhGly)P-(OPh)2 is not observed in the complex. The L-stereoisomer of the inhibitor forms contacts with several residues in the trypsin active site. One of the phosphonate oxygens is inserted into the oxyanion hole and forms hydrogen bonds to the amides of Gly193, Asp194, and Ser195. The second phosphonate oxygen forms hydrogen bonds to N epsilon 2 of His 57. The p-amidinophenylglycine moiety binds into the trypsin primary specificity pocket, interacting with Asp189. The amide forms a hydrogen bond to the carbonyl oxygen atom of Ser214. The inhibitor moiety, from the 113 K structure of trypsin inactivated by the reaction product of Z-(4-AmPhGly)P(OPh)2, was docked into human thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., & Hofsteenge, J. (1989) EMBO J. 8, 3467-3475] and energy minimized. The inhibitor fits well into the thrombin active site, forming favorable contacts similar to those in the trypsin complex with no bad contacts.

PubMed: 8605148
DOI: 10.1021/bi9520996

Experimental method

X-RAY DIFFRACTION (1.8 Å)