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The crystal structure of yeast copper thionein: the solution of a long-lasting enigma.

ABSTRACT: We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-A resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven rather than eight metal ions. The protein backbone has a random coil structure with the loops enfolding the copper cluster, which is located in a cleft where it is bound to 10 cysteine residues. The protein structure is somewhat different from that of Ag(7)-MT and similar, but not identical, to that of Cu(7)-MT. Besides the different structure of the metal cluster, the main differences lie in the cysteine topology and in the conformation of some portions of the backbone. The present structure suggests that Cu-MT, in addition to its role as a safe depository for copper ions in the cell, may play an active role in the delivery of copper to metal-free chaperones.

SUBMITTER: Calderone V

PROVIDER: S-EPMC544076 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature

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The crystal structure of yeast copper thionein: the solution of a long-lasting enigma.

Calderone Vito V Dolderer Benedikt B Hartmann Hans-Juergen HJ Echner Hartmut H Luchinat Claudio C Del Bianco Cristina C Mangani Stefano S Weser Ulrich U

Proceedings of the National Academy of Sciences of the United States of America 20041221 1

We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-A resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven rather than eight metal ions. The protein backbone has a random coil structure with the loops enfold ...[more]

PMID: 15613489

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Project description:The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the positions of the crystallographic water molecules were compared to peaks in the MD density after alignment of the protein in each snapshot. The results of this analysis indicate that all simulations reproduce the crystallographic water structure rather poorly. However, if we define the crystallographic water sites based on their distances to nearby protein atoms and follow these sites throughout the simulations, the MD simulations reproduce the crystallographic water sites much better. This shows that the failure of MD simulations to reproduce the water structure around proteins in crystal structures observed both in this and previous studies is caused by the problem of identifying water sites for a flexible and dynamic protein (traditionally done by overlaying the structures). Our local clustering approach solves the problem and shows that the MD simulations reasonably reproduce the water structure observed in crystals. Furthermore, analysis of the crystal MD simulations indicates a few water molecules that are close to unmodeled electron density peaks in the crystal structures, suggesting that crystal MD could be used as a complementary tool for identifying and modelling water in protein crystallography.

Dataset Information

The crystal structure of yeast copper thionein: the solution of a long-lasting enigma.

Publications

The crystal structure of yeast copper thionein: the solution of a long-lasting enigma.

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