3D40

Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with diphosphate

3D40 の概要

• エントリーDOI: 10.2210/pdb3d40/pdb
• 関連するPDBエントリー: 3D41
• 分子名称: FomA protein, DIPHOSPHATE (3 entities in total)
• 機能のキーワード: fosfomycin, antibiotic resistance, kinase, phosphoryl transfer, transferase
• 由来する生物種: Streptomyces wedmorensis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 31050.79

構造登録者

Pakhomova, S.,Bartlett, S.G.,Augustus, A.,Kuzuyama, T.,Newcomer, M.E. (登録日: 2008-05-13, 公開日: 2008-08-12, 最終更新日: 2024-04-03)

主引用文献

Pakhomova, S.,Bartlett, S.G.,Augustus, A.,Kuzuyama, T.,Newcomer, M.E.
Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.
J.Biol.Chem., 283:28518-28526, 2008

PubMed Abstract: 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'-(beta,gamma-imido)-triphosphate (AMPPNP), Mg(II), and fosfomycin, at 1.53 and 2.2 angstroms resolution, respectively. The polypeptide exhibits an open alphabetaalpha 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 alpha2-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 beta- and gamma-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 (5.1 angstroms) between the phosphate acceptor and donor groups in FomA, and involvement of Lys18 instead of Lys9 in binding with the gamma-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.

PubMed: 18701452
DOI: 10.1074/jbc.M803709200

実験手法

X-RAY DIFFRACTION (1.53 Å)