Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis

• Published in: The Journal of biological chemistry Vol. 283; no. 42; pp. 28518 - 28526
• Main Authors: Pakhomova, Svetlana, Bartlett, Sue G., Augustus, Alexandria, Kuzuyama, Tomohisa, Newcomer, Marcia E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17.10.2008; American Society for Biochemistry and Molecular Biology
• Subjects: Adenylyl Imidodiphosphate - chemistry; Amino Acid Sequence; Bacterial Proteins - chemistry; Catalytic Domain; Crystallography, X-Ray; Drug Resistance, Bacterial; Fosfomycin - pharmacology; Lysine - chemistry; Molecular Conformation; Molecular Sequence Data; Phosphotransferases (Phosphate Group Acceptor) - chemistry; Protein Conformation; Protein Structure, Quaternary; Pseudomonas aeruginosa - metabolism; Sequence Homology, Amino Acid; Streptomyces - metabolism; Substrate Specificity
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M803709200

The fosfomycin resistance protein FomA inactivates fosfomycin by phosphorylation of the phosphonate group of the antibiotic in the presence of ATP and Mg(II). We report the crystal structure of FomA from the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis in complex with diphosphate and in ternary complex with the nonhydrolyzable ATP analog adenosine 5′-(β,γ-imido)-triphosphate (AMPPNP), Mg(II), and fosfomycin, at 1.53 and 2.2Å resolution, respectively. The polypeptide exhibits an open αβα sandwich fold characteristic for the amino acid kinase family of enzymes. The diphosphate complex shows significant disorder in loops surrounding the active site. As a result, the nucleotide-binding site is wide open. Binding of the substrates is followed by the partial closure of the active site and ordering of the α2-helix. Structural comparison with N-acetyl-l-glutamate kinase shows several similarities in the site of phosphoryl transfer: 1) preservation of architecture of the catalytical amino acids of N-acetyl-l-glutamate kinase (Lys9, Lys216, and Asp150 in FomA); 2) good superposition of the phosphate acceptor groups of the substrates, and 3) good superposition of the diphosphate molecule with the β- and γ-phosphates of AMPPNP, suggesting that the reaction could proceed by an associative in-line mechanism. However, differences in conformations of the triphosphate moiety of AMPPNP molecules, the long distance (5.1Å) between the phosphate acceptor and donor groups in FomA, and involvement of Lys18 instead of Lys9 in binding with the γ-phosphate may indicate a different reaction mechanism. The present work identifies the active site residues of FomA responsible for substrate binding and specificity and proposes their roles in catalysis.