title: Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated.
abstract: The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation.
authors.affiliation: Nuclear, Biological and Chemical Detection Technology Section, Human Oriented Systems Division, Advanced Defense Technology Center, Technical Research and Development Institute, Ministry of Defense, Meguro, Tokyo 153-8630, Japan. mas@cs.trdi.mod.go.jp
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Masuda
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Nitanai
authors.forename: Ryuta
authors.initials: R
authors.lastname: Mizutani
authors.forename: Shuji
authors.initials: S
authors.lastname: Noguchi
mesh_terms: D000215:Acylation; D000818:Animals; D020134:Catalytic Domain; D002417:Cattle; D018360:Crystallography, X-Ray / Q000379:methods; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D050050:Protein Carbonylation; D011487:Protein Conformation; D014357:Trypsin / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D046911:Macromolecular Substances; D014867:Water; D014357:Trypsin; D010100:Oxygen