Abstract / Summary
The lineages of the Mycobacterium tuberculosis complex (MTBC) that returned to a human host after the animal radiation, L6 together with L9 and L10, share a small set of fixed variants. One of them, NC_000962.3:2894321:G:C (c.87C>G, p.Asp29Glu), falls in Rv2569c (melE), a macrophage-infection protease of the transglutaminase family described since 2004 and carrying the strongest in vivo phenotype signal; I asked whether it does anything. Across 142 673 genomes assigned to 705 clades, the variant is carried by 1400 of the 1402 genomes of the L6+L9+L10 node, the two exceptions being low-coverage false negatives (lowest call counts and read depth in their sub-clade), so 1400/1400 informative members; and by 1 of the 141 271 genomes outside the node, a homoplasy (ordinary-quality genome). It is the only fixed non-synonymous change of the gene in that clade, and the rest of the mel1 locus carries none. Residue 29 lies 31.9 Å (C[[EQUATION]]-C[[EQUATION]]) from the catalytic nucleophile Cys196, placed by two independent routes; the general base and acid are a moderate-confidence hypothesis. The residue is not in the disordered region a sequence predictor had declared, but in a folded, exposed domain (pLDDT 95.7) devoid of any detectable binding pocket, ranking last of 312 residues for cryptic-pocket propensity, the catalytic triad (positive control) ranking in the first tenth. Its predicted impact is below the median of 26 matched controls from the same set (S6). The substitution is therefore a near-perfect diagnostic marker for a node that no barcode currently names, with no effect detectable by any measure able to detect one. I also correct three parameters of melE: its catalytic class is transglutaminase-like rather than serine, its numbered active site is reported for the first time, and its disputed in vivo role resolves as host-genetic-background dependence, not a disagreement between methods.