Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family

Abstract

The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn²⁺-ion have been presented. The 152 amino acid protein consists of two similar domains with α + β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a twofold pseudo-symmetry rotation axis. A sequence homology search identified the protein as a member of the structural family Glyoxalase I. We have shown that the enzyme possesses glyoxalase I activity in the presence of Zn²⁺, Mg²⁺, Ni²⁺, and Co²⁺, in this order of preference. Sequence and structure comparisons revealed that human glyoxalase I should be assigned to a subfamily A, while S. aureus glyoxalase I represents a new subfamily B, which includes also proteins from other bacteria. Both subfamilies have a similar protein chain fold but rather diverse sequences. The active sites of human and staphylococcus glyoxalases I are also different: the former contains one Zn-ion per chain; the latter incorporates two of these ions. In the active site of SA0856, the first Zn-ion is well coordinated by His58, Glu60 from basic molecule and Glu40*, His44* from adjacent symmetry-related molecule. The second Zn3-ion is coordinated only by residue His143 from protein molecule and one acetate ion. We suggest that only single Zn1-ion plays the role of catalytic center. The newly found differences between the two subfamilies could guide the design of new drugs against S. aureus, an important pathogenic micro-organism.

Keywords:

• metalloprotein
• glyoxalase I
• subfamily
• pathogen

Acknowledgements

We express our gratitude to Prof. Tom Blundell, FRS, and Dr. Dmitri Chirgadze, Cambridge University, UK, for their valuable help and support in performing activity assays of Zn-glyoxalase I. EFP acknowledges support from the Canada Research Chairs program. Contract grant sponsors: Ontario Research and Development Challenge Fund (contract No. 99-SEP-0512). Use of the IMCA-CAT beam line 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the Hauptman-Woodward Medical Research Institute. This research used resources of the Advanced Photon Source, a US Department of Energy Office of Science User Facility operated for the DOE Office of Science by Argonne National laboratory under contract No. DE-AC02-06CH11357.

Disclosure statement

No potential conflict of interest was reported by the authors.