1OEW

ATOMIC RESOLUTION STRUCTURE OF NATIVE ENDOTHIAPEPSIN

Summary for 1OEW

• Entry DOI: 10.2210/pdb1oew/pdb
• Related: 1E5O 1E80 1E81 1E82 1EED 1ENT 1EPL 1EPM 1EPN 1EPO 1EPP 1EPQ 1EPR 1ER8 1GKT 1GVT 1GVU 1GVV 1GVW 1GVX 1OD1 1OEX 2ER0 2ER6 2ER7 2ER9 3ER3 3ER5 4APE 4ER1 4ER2 4ER4 5ER1 5ER2
• Descriptor: ENDOTHIAPEPSIN, SERINE, THREONINE, ... (6 entities in total)
• Functional Keywords: hydrolase, aspartic proteinase mechanism, atomic resolution, succinimide, anisotropic refinement
• Biological source: CRYPHONECTRIA PARASITICA (CHESTNUT BLIGHT FUNGUS)
• Total number of polymer chains: 1
• Total formula weight: 34592.46

Authors

Coates, L.,Erskine, P.T.,Mall, S.,Gill, R.S.,Wood, S.P.,Myles, D.A.A.,Cooper, J.B. (deposition date: 2003-03-31, release date: 2003-04-02, Last modification date: 2023-11-15)

Primary citation

Erskine, P.T.,Coates, L.,Mall, S.,Gill, R.S.,Wood, S.P.,Myles, D.A.A.,Cooper, J.B.
Atomic Resolution Analysis of the Catalytic Site of an Aspartic Proteinase and an Unexpected Mode of Binding by Short Peptides
Protein Sci., 12:1741-, 2003

PubMed Abstract: The X-ray structures of native endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 A resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.

PubMed: 12876323
DOI: 10.1110/PS.0305203

Experimental method

X-RAY DIFFRACTION (0.9 Å)