The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes.

Abstract

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, continues to be a major threat to populations worldwide. Whereas the disease is treatable, the drug regimen is arduous at best with the use of four antimicrobials over a six-month period. There is clearly a pressing need for the development of new therapeutics. One potential target for structure-based drug design is the enzyme RmlA, a glucose-1-phosphate thymidylyltransferase. This enzyme catalyzes the first step in the biosynthesis of l-rhamnose, which is a deoxysugar critical for the integrity of the bacterium's cell wall. Here, we report the X-ray structures of M. tuberculosis RmlA in complex with either dTTP or dTDP-glucose to 1.6 Å and 1.85 Å resolution, respectively. In the RmlA/dTTP complex, two magnesium ions were observed binding to the nucleotide, both ligated in octahedral coordination spheres. In the RmlA/dTDP-glucose complex, only a single magnesium ion was observed. Importantly, for RmlA-type enzymes with known three-dimensional structures, not one model shows the position of the magnesium ion bound to the nucleotide-linked sugar. As such, this investigation represents the first direct observation of the manner in which a magnesium ion is coordinated to the RmlA product and thus has important ramifications for structure-based drug design. In the past, molecular modeling procedures have been employed to derive a three-dimensional model of the M. tuberculosis RmlA for drug design. The X-ray structures presented herein provide a superior molecular scaffold for such endeavors in the treatment of one of the world's deadliest diseases.

• Authors: Haley A Brown, James B Thoden, Peter A Tipton, Hazel M Holden
• Journal: Protein science : a publication of the Protein Society (Protein Sci) Vol. 27 Issue 2 Pg. 441-450 (02 2018) ISSN: 1469-896X [Electronic] United States
• PMID: 29076563 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)
• Copyright: © 2017 The Protein Society.

Chemical References

• Bacterial Proteins
• Thymine Nucleotides
• deoxythymidine diphosphate-glucose
• Nucleotidyltransferases
• glucose-1-phosphate thymidylyltransferase
• Magnesium
• Glucose
• thymidine 5'-triphosphate

Topics

• Allosteric Site
• Bacterial Proteins (chemistry, metabolism)
• Crystallography, X-Ray
• Glucose (analogs & derivatives, metabolism)
• Magnesium (chemistry)
• Models, Molecular
• Mycobacterium tuberculosis (chemistry, enzymology, genetics)
• Nucleotidyltransferases (chemistry, genetics, metabolism)
• Protein Binding
• Protein Conformation
• Thymine Nucleotides (metabolism)