3TM0

Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Butirosin A Complex

Replaces:  3H8P

Summary for 3TM0

• Entry DOI: 10.2210/pdb3tm0/pdb
• Related: 1J7I 1J7L 1J7U 1L8T 2B0Q 3TL7
• Descriptor: Aminoglycoside 3'-phosphotransferase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, (2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide, ... (5 entities in total)
• Functional Keywords: protein kinase, phosphorylation, transferase-antibiotic complex, transferase/antibiotic
• Biological source: Enterococcus faecalis
• Total number of polymer chains: 1
• Total formula weight: 31991.23

Authors

Berghuis, A.M.,Fong, D.H. (deposition date: 2011-08-30, release date: 2011-10-19, Last modification date: 2023-09-13)

Primary citation

Fong, D.H.,Berghuis, A.M.
Structural basis of APH(3')-IIIa-mediated resistance to N1-substituted aminoglycoside antibiotics.
Antimicrob.Agents Chemother., 53:3049-3055, 2009

PubMed Abstract: Butirosin is unique among the naturally occurring aminoglycosides, having a substituted amino group at position 1 (N1) of the 2-deoxystreptamine ring with an (S)-4-amino-2-hydroxybutyrate (AHB) group. While bacterial resistance to aminoglycosides can be ascribed chiefly to drug inactivation by plasmid-encoded aminoglycoside-modifying enzymes, the presence of an AHB group protects the aminoglycoside from binding to many resistance enzymes, and hence, the antibiotic retains its bactericidal properties. Consequently, several semisynthetic N1-substituted aminoglycosides, such as amikacin, isepamicin, and netilmicin, were developed. Unfortunately, butirosin, amikacin, and isepamicin are not resistant to inactivation by 3'-aminoglycoside O-phosphotransferase type IIIa [APH(3')-IIIa]. We report here the crystal structure of APH(3')-IIIa in complex with an ATP analog, AMPPNP [adenosine 5'-(beta,gamma-imido)triphosphate], and butirosin A to 2.4-A resolution. The structure shows that butirosin A binds to the enzyme in a manner analogous to other 4,5-disubstituted aminoglycosides, and the flexible antibiotic-binding loop is key to the accommodation of structurally diverse substrates. Based on the crystal structure, we have also constructed a model of APH(3')-IIIa in complex with amikacin, a commonly used semisynthetic N1-substituted 4,6-disubstituted aminoglycoside. Together, these results suggest a strategy to further derivatize the AHB group in order to generate new aminoglycoside derivatives that can elude inactivation by resistance enzymes while maintaining their ability to bind to the ribosomal A site.

PubMed: 19433564
DOI: 10.1128/AAC.00062-09

Experimental method

X-RAY DIFFRACTION (2.1 Å)