PDBsum entry 5er2

Hydrolase/hydrolase inhibitor

PDB id: 5er2

Contents

Protein chain

330 a.a. *

Ligands

0EK

Waters ×246

* Residue conservation analysis

PDB id:

5er2

Name:

Hydrolase/hydrolase inhibitor

Title:

High-resolution x-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. The analysis of the inhibitor binding and description of the rigid body shift in the enzyme

Structure:

Endothiapepsin. Chain: e. Engineered: yes

Source:

Cryphonectria parasitica. Chestnut blight fungus. Organism_taxid: 5116

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.160

Authors:

A.Sali,B.Veerapandian,J.B.Cooper,S.I.Foundling,D.J.Hoover, T.L.Blundell

Key ref:

A.Sali et al. (1989). High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme. Embo J, 8, 2179-2188. PubMed id: 2676515

Date:

02-Jan-91 Release date: 15-Apr-91

Protein chain

P11838  (CARP_CRYPA) -  Endothiapepsin from Cryphonectria parasitica

Seq: 419 a.a.

Struc: 330 a.a.

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.

Embo J 8:2179-2188 (1989)

PubMed id: 2676515

High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.

A.Sali, B.Veerapandian, J.B.Cooper, S.I.Foundling, D.J.Hoover, T.L.Blundell.

ABSTRACT

The conformation of the synthetic renin inhibitor CP-69,799, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 1.8 A resolution and refined to the crystallographic R factor of 16%. CP-69,799 is an oligopeptide transition--state analogue inhibitor that contains a new dipeptide isostere at the P1-P1' position. This dipeptide isostere is a nitrogen analogue of the well-explored hydroxyethylene dipeptide isostere, wherein the tetrahedral P1' C alpha atom has been replaced by trigonal nitrogen. The inhibitor binds in the extended conformation, filling S4 to S3' pockets, with hydroxyl group of the P1 residue positioned symmetrically between the two catalytic aspartates of the enzyme. Interactions between the inhibitor and the enzyme include 12 hydrogen bonds and extensive van der Waals contacts in all the pockets, except for S3'. The crystal structure reveals a bifurcated orientation of the P2 histidine side chain and an interesting relative rotation of the P3 phenyl ring to accommodate the cyclohexyl side chain at P1. The binding of the inhibitor to the enzyme, while producing no large distortions in the enzyme active site cleft, results in small but significant change in the relative orientation of the two endothiapepsin domains. This structural change may represent the action effected by the proteinase as it distorts its substrate towards the transition state for proteolytic cleavage.