Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis

Shan Gao, Fangyu Wu, Sudagar S Gurcha, Sarah M Batt, Gurdyal S Besra*, Zihe Rao*, Lu Zhang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

In Mycobacterium tuberculosis, Rv3806c is a membrane-bound phosphoribosyltransferase (PRTase) involved in cell wall precursor production. It catalyses pentosyl phosphate transfer from phosphoribosyl pyrophosphate to decaprenyl phosphate, to generate 5-phospho-β-ribosyl-1-phosphoryldecaprenol. Despite Rv3806c being an attractive drug target, structural and molecular mechanistic insight into this PRTase is lacking. Here we report cryogenic electron microscopy structures for Rv3806c in the donor- and acceptor-bound states. In a lipidic environment, Rv3806c is trimeric, creating a UbiA-like fold. Each protomer forms two helical bundles, which, alongside the bound lipids, are required for PRTase activity in vitro. Mutational and functional analyses reveal that decaprenyl phosphate and phosphoribosyl pyrophosphate bind the intramembrane and extramembrane cavities of Rv3806c, respectively, in a distinct manner to that of UbiA superfamily enzymes. Our data suggest a model for Rv3806c-catalysed phosphoribose transfer through an inverting mechanism. These findings provide a structural basis for cell wall precursor biosynthesis that could have potential for anti-tuberculosis drug development.

Original languageEnglish
JournalNature Microbiology
Early online date15 Mar 2024
DOIs
Publication statusE-pub ahead of print - 15 Mar 2024

Bibliographical note

Acknowledgments:
We thank W. Xu from ShanghaiTech University for discussion of the manuscript. We thank L. Wang and Q. Sun from the Bio-Electron Microscopy Facility and J. Chen, W. Zhu and X. Gao from Analytical Chemistry Platform of Shanghai Institute for Advanced Immunochemical Studies (SIAIS) of ShanghaiTech University for their support in EM data collection and mass spectrometry analysis respectively. We thank J. Liu at the Protein Preparation and Characterization Platform of Technology Center for Protein Research, Tsinghua University for providing facility support in MMS analysis. We thank J. Li from Large-scale Protein Preparation System at the National Facility for Protein Science in Shanghai (NFPS) for technical support. This work was supported by grants from National Natural Science Foundation of China (grant no. 32394010 to Z.R., and grant no. 32394011 to L.Z.), R&D Program of Guangzhou Laboratory (SRPG22-003) to Z.R. and L.Z., Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Medical Research Council UK (MR/S000542/1 and MR/R001154/1) to G.S.B.

Copyright:
© 2024. The Author(s).

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