PDBsum entry 1pq7

Hydrolase

PDB id: 1pq7

Contents

Protein chain

224 a.a. *

Ligands

SO4 ×2

ARG

Waters ×495

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Trypsin revisited: crystallography at (sub) atomic resolution and quantum chemistry revealing details of catalysis.

Authors

A.Schmidt, C.Jelsch, P.Ostergaard, W.Rypniewski, V.S.Lamzin.

Ref.

J Biol Chem, 2003, 278, 43357-43362. [DOI no: 10.1074/jbc.M306944200]

PubMed id

12937176

Abstract

A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.

Figure 1.
FIG. 1. A, overlay of the active sites in the structures at pH 4 (red), pH 5 (yellow), with PMSF (gray) and DFP (blue), showing the effects of the covalent inhibitors on the catalytic triad. It also shows that different orientations are possible for the substrate. B, the active site in the pH 4 structure, as used for the ab initio calculations. The oxyanion hole is omitted for clarity. The geometry around the substrate arginine carbonyl is roughly tetrahedral and shows unusual interatomic distances. Figures were produced with Molscript/Raster3D (36).

Figure 4.
FIG. 4. Thermal ellipsoids with 35% probability for the catalytic triad of the pH 5 and PMSF structures showing the difference in anisotropy. The figure was produced in XtalView (37).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 43357-43362) copyright 2003.