3I0O

Crystal Structure of Spectinomycin Phosphotransferase, APH(9)-Ia, in complex with ADP and Spectinomcyin

Summary for 3I0O

• Entry DOI: 10.2210/pdb3i0o/pdb
• Descriptor: Spectinomycin phosphotransferase, ADENOSINE-5'-DIPHOSPHATE, SPECTINOMYCIN, ... (6 entities in total)
• Functional Keywords: protein kinase, aminoglycoside phosphotransferase, antibiotic resistance, transferase
• Biological source: Legionella pneumophila serogroup 1
• Total number of polymer chains: 1
• Total formula weight: 40505.38

Authors

Fong, D.H.,Lemke, C.T.,Hwang, J.,Xiong, B.,Berghuis, A.M. (deposition date: 2009-06-25, release date: 2010-01-19, Last modification date: 2024-04-03)

Primary citation

Fong, D.H.,Lemke, C.T.,Hwang, J.,Xiong, B.,Berghuis, A.M.
Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila.
J.Biol.Chem., 285:9545-9555, 2010

PubMed Abstract: Aminoglycoside phosphotransferases (APHs) constitute a diverse group of enzymes that are often the underlying cause of aminoglycoside resistance in the clinical setting. Several APHs have been extensively characterized, including the elucidation of the three-dimensional structure of two APH(3') isozymes and an APH(2'') enzyme. Although many APHs are plasmid-encoded and are capable of inactivating numerous 2-deoxystreptmaine aminoglycosides with multiple regiospecificity, APH(9)-Ia, isolated from Legionella pneumophila, is an unusual enzyme among the APH family for its chromosomal origin and its specificity for a single non-2-deoxystreptamine aminoglycoside substrate, spectinomycin. We describe here the crystal structures of APH(9)-Ia in its apo form, its binary complex with the nucleotide, AMP, and its ternary complex bound with ADP and spectinomycin. The structures reveal that APH(9)-Ia adopts the bilobal protein kinase-fold, analogous to the APH(3') and APH(2'') enzymes. However, APH(9)-Ia differs significantly from the other two types of APH enzymes in its substrate binding area and that it undergoes a conformation change upon ligand binding. Moreover, kinetic assay experiments indicate that APH(9)-Ia has stringent substrate specificity as it is unable to phosphorylate substrates of choline kinase or methylthioribose kinase despite high structural resemblance. The crystal structures of APH(9)-Ia demonstrate and expand our understanding of the diversity of the APH family, which in turn will facilitate the development of new antibiotics and inhibitors.

PubMed: 20089863
DOI: 10.1074/jbc.M109.038364

Experimental method

X-RAY DIFFRACTION (2.4 Å)