Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2′′-phosphotransferases

Abstract

Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2′′) family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). The structure of the ternary complex of APH(2′′)-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2′′)-Ia, APH(2′′)-IIa and APH(2′′)-IVa. In contrast to the case for APH(2′′)-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2′′)-IIa, APH(2′′)-IIIa and APH(2′′)-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.

Ephedra sinica polysaccharide regulate the anti-inflammatory immunity of intestinal microecology and bacterial metabolites in rheumatoid arthritis

“…Bacteria can encode aminoglycoside-modifying enzymes such as acetyl-CoA-dependent aminoglycoside acetyltransferase and ATP/GTP-dependent phosphotransferase (APH). APH confers high levels of resistance to aminoglycoside antibiotics through enzymatic modification ( Smith et al, 2019 ). The APH gene expression gradually increases with an increase in the arabitol concentration, and this increase is consistent with resistance phenotypes ( Zhang et al, 2016 ).…”

Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment

“…In aminoglycosides, modification of the antibiotic molecule occurs due to a group of enzymes that can be divided into three different categories: the acetyl-coenzyme A-dependent amino-glycoside acetyltransferases (AACs), that act through acetylation of the amino groups; the ATP-dependent nucleotidyltransferases (ANTs), that act through adenylation of the hydroxyl group; and the ATP/GTP-dependent phosphotransferases (APHs), that act through phosphorylation of the hydroxyl group [ 9 , 123 ]. These molecules are also divided into sub-groups according to which position is altered (3′, 6′, 2″,3″, 4″, etc.…”

“…Letters (a, b, c, d, e, etc.) were added at the end in order to distinguish each specific protein [ 1 , 123 , 124 ].…”

Identification and characterization of a novel chromosomal aminoglycoside 3’-O-phosphotransferase, APH(3′)-Id, from Kluyvera intermedia DW18 isolated from the sewage of an animal farm

“…It was found that APHs shared similar active sites with eukaryotic protein kinases (ePKs) and common ePK-like folds in the tertiary structure, and the inhibitors of ePKs also showed inhibitory activity against APHs, which suggested that they might have been derived from a common ancestor ( Hon et al, 1997 ; Stogios et al, 2013 ). Some APHs were also found to have NTPs hydrolase activity and can hydrolyze NTPs in the absence of an antibiotic substrate, but the efficiency of NTP hydrolysis was far less than the catalytic efficiency of the antibiotic substrate, so it had little impact on the modification of antibiotics ( Kim C. et al, 2006 ; Smith et al, 2019 ). The APH classes and subclasses include APH(4)-I, APH(6)-I, APH(9)-I, APH(3′)-I through IX, APH(3′)-XV, APH(2″)-I through IV, APH(3″)-I and APH(7″)-I ( Alcock et al, 2023 ).…”