4CMX

Crystal structure of Rv3378c

Summary for 4CMX

• Entry DOI: 10.2210/pdb4cmx/pdb
• Related: 4CMV 4CMW
• Descriptor: RV3378C, BENZENE HEXACARBOXYLIC ACID, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: nuclear protein
• Biological source: MYCOBACTERIUM TUBERCULOSIS
• Total number of polymer chains: 2
• Total formula weight: 69461.80

Authors

Layre, E.,Lee, H.J.,Young, D.C.,Martinot, A.J.,Buter, J.,Minnaard, A.J.,Annand, J.W.,Fortune, S.M.,Snider, B.B.,Matsunaga, I.,Rubin, E.J.,Alber, T.,Moody, D.B. (deposition date: 2014-01-18, release date: 2014-02-19, Last modification date: 2023-12-20)

Primary citation

Layre, E.,Lee, H.J.,Young, D.C.,Jezek Martinot, A.,Buter, J.,Minnaard, A.J.,Annand, J.W.,Fortune, S.M.,Snider, B.B.,Matsunaga, I.,Rubin, E.J.,Alber, T.,Moody, D.B.
Molecular Profiling of Mycobacterium Tuberculosis Identifies Tuberculosinyl Nucleoside Products of the Virulence-Associated Enzyme Rv3378C.
Proc.Natl.Acad.Sci.USA, 111:2978-, 2014

PubMed Abstract: To identify lipids with roles in tuberculosis disease, we systematically compared the lipid content of virulent Mycobacterium tuberculosis with the attenuated vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. Comparative lipidomics analysis identified more than 1,000 molecular differences, including a previously unknown, Mycobacterium tuberculosis-specific lipid that is composed of a diterpene unit linked to adenosine. We established the complete structure of the natural product as 1-tuberculosinyladenosine (1-TbAd) using mass spectrometry and NMR spectroscopy. A screen for 1-TbAd mutants, complementation studies, and gene transfer identified Rv3378c as necessary for 1-TbAd biosynthesis. Whereas Rv3378c was previously thought to function as a phosphatase, these studies establish its role as a tuberculosinyl transferase and suggest a revised biosynthetic pathway for the sequential action of Rv3377c-Rv3378c. In agreement with this model, recombinant Rv3378c protein produced 1-TbAd, and its crystal structure revealed a cis-prenyl transferase fold with hydrophobic residues for isoprenoid binding and a second binding pocket suitable for the nucleoside substrate. The dual-substrate pocket distinguishes Rv3378c from classical cis-prenyl transferases, providing a unique model for the prenylation of diverse metabolites. Terpene nucleosides are rare in nature, and 1-TbAd is known only in Mycobacterium tuberculosis. Thus, this intersection of nucleoside and terpene pathways likely arose late in the evolution of the Mycobacterium tuberculosis complex; 1-TbAd serves as an abundant chemical marker of Mycobacterium tuberculosis, and the extracellular export of this amphipathic molecule likely accounts for the known virulence-promoting effects of the Rv3378c enzyme.

PubMed: 24516143
DOI: 10.1073/PNAS.1315883111

Experimental method

X-RAY DIFFRACTION (2.36 Å)