PDBsum entry 1pqa

Hydrolase

PDB id: 1pqa

Contents

Protein chain

224 a.a. *

Ligands

SO4 ×2

Waters ×270

* Residue conservation analysis

PDB id:

1pqa

Name:

Hydrolase

Title:

Trypsin with pmsf at atomic resolution

Structure:

Trypsin. Chain: a. Ec: 3.4.21.4

Source:

Fusarium oxysporum. Organism_taxid: 5507

Resolution:

1.23Å R-factor: 0.141

Authors:

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

Key ref:

A.Schmidt et al. (2003). Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis. J Biol Chem, 278, 43357-43362. PubMed id: 12937176 DOI: 10.1074/jbc.M306944200

Date:

18-Jun-03 Release date: 11-Nov-03

Protein chain

P35049  (TRYP_FUSOX) -  Trypsin from Fusarium oxysporum

Seq: 248 a.a.

Struc: 224 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1074/jbc.M306944200

J Biol Chem 278:43357-43362 (2003)

PubMed id: 12937176

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

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.