Crystal structure of the putative cell‐wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2022-04, Vol.78 (4), p.494-508
• Main Authors: Patel, Onisha, Brammananth, Rajini, Dai, Weiwen, Panjikar, Santosh, Coppel, Ross L., Lucet, Isabelle S., Crellin, Paul K.
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - metabolism; Biosynthesis; Corynebacterium glutamicum - metabolism; Crystal structure; Elongated structure; Glycolipids; Holes; Homology; Humans; Immune response; Inositol; Inositols; lipoarabinomannan; lipomannan; Lipopolysaccharides - chemistry; Lipopolysaccharides - metabolism; Membrane proteins; Membranes; MSMEG_0317; Mycobacterium smegmatis; Mycobacterium smegmatis - metabolism; Mycobacterium tuberculosis; Mycobacterium tuberculosis - metabolism; Pathogenesis; Protein biosynthesis; Proteins; Research Papers; Structural members; Tuberculosis; Xenon
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798322001772

The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one‐quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl‐myo‐inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface‐exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full‐length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β‐barrel fold enclosing two distinct cavities and one α‐helix extending away from the β‐barrel core, resembling a `cone with a flake' arrangement. Through xenon derivatization and structural comparison with AlphaFold2‐derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from `closed' to `open' conformations, allowing cavity access. An AlphaFold2‐derived NCgl2760 model predicted a smaller β‐barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis. The first crystal structure of the putative cell‐wall biosynthesis protein LmcA from Mycobacterium smegmatis is reported at 1.8 Å resolution. The structure revealed an elongated β‐barrel fold enclosing two distinct cavities, indicating a possible lipid‐binding function in lipomannan/lipoarabinomannan biosynthesis.