Fig. 5
3D model for LMM-PBP4 of PAO1. a Homology modeling of monomer Pseudomonas aeruginosa LMM-PBP4 (surface representation). The different domains are presented in brown (domain I), red (domain II) and green (domain III). b Domain I and conserved motifs in the active site of LMM-PBP4. For the first conserved sequence SxxK (STMK; *S72, catalytic serine at position 72), located at the beginning of α2 helix, residues are represented by an intense, blue, cyan and pale blue color, respectively. The second conserved sequence SxN (SNN), located in a short loop between α3-α4, is represented by a gradient of colors derived from green. The three residues of the third conserved motif KTG, located in a β sheet (β2) are represented on dark red, red and orange, respectively. c Location for synthetic peptide AMV-L-Ala-FGA-L-Lys-D-Ala-D-Ala (linear representation) is indicated within the active site model for LMM-PBP4. Estimated distances for depth, height and width in this cavity are shown. d Putative residues constituents for the specific subsite in the active site of LMM-PBP4. Location of the amino acid lysine (L-Lys) of the synthetic substrate AMV-L-Ala-FGA-L-Lys-D-Ala-D-Ala, the residue equivalent to mesoA2pm in natural muropeptides, is indicated. Each amino acid has been labeled and highlighted by a color (aspartic acid 162, blue; leucine 369, green; threonine 428, yellow; leucine 429, red; asparagine 430, gray). AMV, methyl 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside; FGA, gamma-D-glutamic acid