1PQ5

Trypsin at pH 5, 0.85 A

Summary for 1PQ5

• Entry DOI: 10.2210/pdb1pq5/pdb
• Related: 1FN8 1FY4 1FY5 1GDN 1GDQ 1PPZ 1PQ7 1PQ8 1PQA
• Descriptor: Trypsin, SULFATE ION, ARGININE, ... (4 entities in total)
• Functional Keywords: trypsin, serine protease, catalysis, hydrolase
• Biological source: Fusarium oxysporum
• Cellular location: Secreted: P35049
• Total number of polymer chains: 1
• Total formula weight: 22663.89

Authors

Schmidt, A.,Jelsch, C.,Rypniewski, W.,Lamzin, V.S. (deposition date: 2003-06-18, release date: 2003-11-11, Last modification date: 2017-10-11)

Primary citation

Schmidt, A.,Jelsch, C.,Ostergaard, P.,Rypniewski, W.,Lamzin, V.S.
Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS.
J.Biol.Chem., 278:43357-43362, 2003

PubMed 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.

PubMed: 12937176
DOI: 10.1074/jbc.M306944200

Experimental method

X-RAY DIFFRACTION (0.85 Å)