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Bioinformatics Project by Jake LeVieux, Spring 2013

AprD4 is an enzyme from a few Streptomyces species that is essential in the biosynthesis of antibiotics tobramycin and apramycin. These antibiotics cause mistranslation and inhibition of bacterial ribosomes. [1] The enzyme is responsible for the removal of the 3' hydroxyl groups (their absence is indicated by * in the structures below), a reaction that allows the antibiotics to be less prone to resistance. [2]


The biosynthetic pathway to tobramycin and apramycin has not been empirically established and the identification of the substrates and products of the reaction will contribute to the knowledge of the sequence of reactions to produce these antibiotics. Additionally, 3' dehydroxylation facilitated by AprD4 likely proceeds through a unique chemical mechanism. Characterization of AprD4 and study of the enzyme mechanism is my current research focus.

This project evaluates the hypothesis that AprD4 might bind a second Fe-S cluster by using a structure prediction tool.

AprD4 Structure-Function prediction

Additionally, the project compares the apr and tob biosynthetic gene clusters to other aminoglycoside gene clusters to study the evolution of aminoglycoside biosynthetic genes.

Phylogeny of aminoglycoside gene clusters

Finally, this project examines the phylogeny of AprD4 by comparing the gene to its closest homologs.

Phylogeny of AprD4

[1] Arya, D., Aminoglycoside Antibiotics : From Chemical Biology to Drug Discovery (2007) Wiley-Interscience
[2] Kondo, S.; Hotta, K. Semisynthetic aminoglycoside antibiotics: development and enzymatic modifications. J. Invect. Chemother. (1999) 5, 1