Acta Crystallographica Section D

Biological Crystallography

Volume 58, Part 9 (September 2002)

research papers

Acta Cryst. (2002). D58, 1448-1461 [ doi:10.1107/S0907444902011769 ]

Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination

R. Thaimattam, E. Tykarska, A. Bierzynski, G. M. Sheldrick and M. Jaskolski

Abstract: CMTI-I, a small-protein trypsin inhibitor, has been crystallized as a 4:1 protein-zinc complex. The metal is coordinated in a symmetric tetrahedral fashion by glutamate/glutamic acid side chains. The structure was solved by direct methods in the absence of prior knowledge of the special position metal centre and refined with anisotropic displacement parameters using diffraction data extending to 1.03 Å. In the final calculations, the main-chain atoms of low B_eq values were refined without restraint control. The two molecules in the asymmetric unit have a conformation that is very similar to that reported earlier for CMTI-I in complex with trypsin, despite the Met8Leu mutation of the present variant. The only significant differences are in the enzyme-binding epitope (including the Arg5 residue) and in a higher mobility loop around Glu24. The present crystal structure contains organic solvent molecules (glycerol, MPD) that interact with the inhibitor molecules in an area that is at the enzyme-inhibitor interface in the CMTI-I-trypsin complex. A perfectly ordered residue (Ala18) has an unusual Ramachandran conformation as a result of geometrical strain introduced by the three disulfide bridges that clamp the protein fold. The results confirm deficiencies of some stereochemical restraints, such as peptide planarity or the N-C-C angle, and suggest a link between their violations and hydrogen bonding.

PDB reference: 1lu0

Keywords: Cucurbita maxima trypsin inhibitor; protease inhibitors; atomic resolution; serine proteases; stereochemical restraints; hydrogen bonding; metal coordination in proteins.