4DTB

Crystal Structure of F95Y Aminoglycoside-2''-Phosphotransferase Type IVa in Complex with Guanosine

Summary for 4DTB

• Entry DOI: 10.2210/pdb4dtb/pdb
• Related: 4DT8 4DT9 4DTA
• Descriptor: APH(2'')-Id, GUANOSINE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: aminoglycoside kinase, transferase
• Biological source: Enterococcus casseliflavus
• Total number of polymer chains: 2
• Total formula weight: 73627.04

Authors

Shi, K.,Berghuis, A.M. (deposition date: 2012-02-20, release date: 2012-03-07, Last modification date: 2024-02-28)

Primary citation

Shi, K.,Berghuis, A.M.
Structural Basis for Dual Nucleotide Selectivity of Aminoglycoside 2''-Phosphotransferase IVa Provides Insight on Determinants of Nucleotide Specificity of Aminoglycoside Kinases.
J.Biol.Chem., 287:13094-13102, 2012

PubMed Abstract: Enzymatic phosphorylation through a family of enzymes called aminoglycoside O-phosphotransferases (APHs) is a major mechanism by which bacteria confer resistance to aminoglycoside antibiotics. Members of the APH(2″) subfamily are of particular clinical interest because of their prevalence in pathogenic strains and their broad substrate spectra. APH(2″) enzymes display differential preferences between ATP or GTP as the phosphate donor, with aminoglycoside 2″-phosphotransferase IVa (APH(2″)-IVa) being a member that utilizes both nucleotides at comparable efficiencies. We report here four crystal structures of APH(2″)-IVa, two of the wild type enzyme and two of single amino acid mutants, each in complex with either adenosine or guanosine. Together, these structures afford a detailed look at the nucleoside-binding site architecture for this enzyme and reveal key elements that confer dual nucleotide specificity, including a solvent network in the interior of the nucleoside-binding pocket and the conformation of an interdomain linker loop. Steady state kinetic studies, as well as sequence and structural comparisons with members of the APH(2″) subfamily and other aminoglycoside kinases, rationalize the different substrate preferences for these enzymes. Finally, despite poor overall sequence similarity and structural homology, analysis of the nucleoside-binding pocket of APH(2″)-IVa shows a striking resemblance to that of eukaryotic casein kinase 2 (CK2), which also exhibits dual nucleotide specificity. These results, in complement with the multitude of existing inhibitors against CK2, can serve as a structural basis for the design of nucleotide-competitive inhibitors against clinically relevant APH enzymes.

PubMed: 22371504
DOI: 10.1074/jbc.M112.349670

Experimental method

X-RAY DIFFRACTION (2.1 Å)