PDBsum entry 2vs2

Hydrolase/hydrolase inhibitor

PDB id: 2vs2

Contents

Protein chain

329 a.a. *

Ligands

0QS

DOD ×220

* Residue conservation analysis

PDB id:

2vs2

Name:

Hydrolase/hydrolase inhibitor

Title:

Neutron diffraction structure of endothiapepsin in complex with a gem- diol inhibitor.

Structure:

Endothiapepsin. Chain: a. Synonym: aspartate protease. Other_details: succinamide is formed between chain a residues 54 and 55.Similar to PDB 1gkt.

Source:

Cryphonectria parasitica. Chestnut blight fungus. Organism_taxid: 5116. Other_details: endothia parasitica formula weight 33814.2

Authors:

L.Coates,H.-F.Tuan,S.Tomanicek,A.Kovalevsky,M.Mustyakimov,P.Erskine, J.Cooper

Key ref:

L.Coates et al. (2008). The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. J Am Chem Soc, 130, 7235-7237. PubMed id: 18479128

Date:

17-Apr-08 Release date: 27-May-08

Protein chain

P11838  (CARP_CRYPA) -  Endothiapepsin from Cryphonectria parasitica

Seq: 419 a.a.

Struc: 329 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.23.22 - endothiapepsin.
• Reaction: Hydrolysis of proteins with broad specificity similar to that of pepsin A, preferring hydrophobic residues at P1 and P1', but does not cleave 14-Ala-|-Leu-15 in the B chain of insulin or Z-Glu-Tyr. Clots milk.

J Am Chem Soc 130:7235-7237 (2008)

PubMed id: 18479128

The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction.

L.Coates, H.F.Tuan, S.Tomanicek, A.Kovalevsky, M.Mustyakimov, P.Erskine, J.Cooper.

ABSTRACT

Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.