Featured Article - May 2011
Short description: The crystal structure of the bacterial cell wall recycling protein Mpl reveals similarities as well as differences compared with functionally related Mur ligases.
Bacterial cell walls contain peptidoglycan (murein), which is synthesized de novo by enzymes of the Mur family. In Gram-negative bacteria, ∼30–60% of the bacterial cell wall is recycled via a process that involves the murein peptide ligase (Mpl), which attaches a breakdown product, the tripeptide L-Ala-γ-Glu-meso-A2pm (it can also attach tetra- and pentapeptides, but less efficiently), to UDP-N-acetylmuramic acid (UDP-MurNAc). Mpl is functionally similar to MurC, as both enzymatic mechanisms involve the ATP-dependent ligation of an amino acid (in the case of MurC) or peptide (in the case of Mpl) to UDP-MurNAc.
Das and colleagues (PSI JCSG) have determined the crystal structure of the first full-length apo Mpl protein from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl) at 1.65-Å resolution. PaMpl can be divided into three distinct domains: the N-terminal UDP-MurNAc–binding domain (ND), the middle ATP-binding domain (MD) and the C-terminal tripeptide-binding domain (CD), which are linked contiguously to from a triangular-shaped molecule. Although PaMpl is larger than MurC from Escherichia coli (EcMurC), with major insertions in the MD, they share a common structural core. The largest conformational difference is in the position of the structurally flexible CD in PaMpl, which is rotated 30° relative to ND and MD, compared with MurC. PaMpl is a monomer in the crystal asymmetric unit but is thought to be dimeric in solution. EcMurC is a dimer in the crystal structure, but exists in a dynamic equilibrium between monomers and dimers in solution. The residues involved in dimerization in PaMpl probably differ from those involved in EcMurC dimerization, suggesting that the mode of dimerization might also be different.
Residues in the ND and MD that are important for interaction with UDP-MurNAc, ATP and metal cofactor have been described for Mur enzymes, and many of these residues are structurally conserved in PaMpl. As true for MurC, PaMpl activity is dependent on magnesium, although no Mg2+ is observed in the PaMpl structure. One metal-binding site is conserved, whereas the region comprising a second metal-binding site is disordered—probably owing to the absence of Mg2+. A loop from CD is folded into part of the ATP- and UDP-MurNAc–binding site, and the authors suggest that a significant conformational change is likely to occur in this region upon binding of substrates and cofactors, thereby ordering the second metal-binding site and opening the CD.
CD is the least conserved domain between Mpl and MurC, which probably reflects their different substrate specificities. Conserved, solvent-exposed Mpl-specific residues in the CD are likely to be important for substrate specificity. The authors identified a number of residues that, upon substrate binding, are likely to induce a conformational change of the CD with respect to the ND and MD. This conformational change is thought to allow UDP-MurNAc to bind to the ND and the tripeptide to access and be positioned at the active site.
These data provide the basis for more extensive functional characterization of Mpl proteins. Given the parallels with Mur enzymes, which are established drug discovery targets, this might lead to the design of better Mur inhibitors that could block both the de novo and recycling pathways for cell wall synthesis, and thereby act as effective antimicrobial agents.
D. Das et al. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.
PLoS One 6, e17624 (2011). doi:10.1371/journal.pone.0017624