5KEF

Structure of hypothetical Staphylococcus protein SA0856 with zinc

Summary for 5KEF

• Entry DOI: 10.2210/pdb5kef/pdb
• Related: 3L20
• Descriptor: PhnB protein, ZINC ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: glyoxalase, metalloprotein, metal binding protein
• Biological source: Staphylococcus aureus subsp. aureus CN1
• Total number of polymer chains: 2
• Total formula weight: 35313.71

Authors

Battaile, K.P.,Chirgadze, Y.N.,Lam, R.,Chan, T.,Mihajlovic, V.,Romanov, V.,Pai, E.,Mendez, V.,Chirgadze, N.Y. (deposition date: 2016-06-09, release date: 2017-01-18, Last modification date: 2024-03-06)

Primary citation

Chirgadze, Y.N.,Boshkova, E.A.,Battaile, K.P.,Mendes, V.G.,Lam, R.,Chan, T.S.Y.,Romanov, V.,Pai, E.F.,Chirgadze, N.Y.
Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family.
J. Biomol. Struct. Dyn., 36:376-386, 2018

PubMed Abstract: The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn-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 Zn, Mg, Ni, and Co, 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.

PubMed: 28034013
DOI: 10.1080/07391102.2016.1278038

Experimental method

X-RAY DIFFRACTION (2.23 Å)