Actinobacteria such as Mycobacterium tuberculosis use the unique thiol mycothiol (MSH) as their primary reducing agent and in the detoxification of xenobiotics. N-Acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) is the metal-dependent deacetylase that catalyzes the deacetylation of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside, the committed step in MSH biosynthesis. We previously used docking studies to identify specific side chains that may contribute as molecular determinants of MshB substrate specificity [Huang, X., and Hernick, M. (2014) Biopolymers 101, 406-417]. Herein, we probe the molecular basis of N-acetylglucosamine (GlcNAc) recognition and turnover by MshB using a combination of site-directed mutagenesis and kinetic studies (mutants examined, L19A, E47A, R68A, D95A, M98A, D146N, and F216A). Results from these studies indicate that MshB is unable to catalyze the turnover of GlcNAc upon loss of the Arg68 or Asp95 side chains, consistent with the proposal that these side chains make critical hydrogen bonding interactions with substrate. The activity of the D146N mutant is ∼10-fold higher than that of the D146A mutant, suggesting that the ability to accept a hydrogen bond at this position contributes to GlcNAc substrate specificity. Because there does not appear to be a direct contact between Asp146 and substrate, this effect is likely mediated via positioning of other catalytically important residues. Finally, we probed side chains located on mobile loops and in a hydrophobic cavity and identified two additional side chains (Met98 and Glu47) that contribute to GlcNAc recognition and turnover by MshB. Together, results from these studies confirm some of the molecular determinants of GlcNAc substrate specificity by MshB, which should aid the development of MshB inhibitors.