Get access

Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated

Authors

  • Yosuke Masuda,

    Corresponding author
    1. 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
    2. Department of Bio-molecular Functions, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
    • Human Oriented Systems Division, Advanced Defense Technology Center, Technical Research and Development Institute, Ministry of Defense, 2-2-1, Naka-meguro, Meguro-ku, Tokyo 153-8630, Japan
    Search for more papers by this author
  • Yasushi Nitanai,

    1. Department of Bio-molecular Functions, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
    Search for more papers by this author
  • Ryuta Mizutani,

    1. Department of Bio-molecular Functions, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
    2. Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
    Search for more papers by this author
  • Shuji Noguchi

    1. Department of Bio-molecular Functions, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
    2. School of Pharmaceutical Sciences, University of Shizuoka, Suruga-Ku, Shizuoka 422-8526, Japan
    Search for more papers by this author

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. Proteins 2013. © 2012 Wiley Periodicals, Inc.

Ancillary