Structural and enzymatic characterization of bacterial cell wall enzymes: Focus on penicillin-binding proteins

The research presented in this dissertation was aimed at understanding several structural and biochemical features underlying the bacterial cell wall biosynthetic process using statistical, biochemical and analytical tools. Penicillin-binding proteins (PBPs) are ubiquitous and essential enzymes necessary for cell wall biosynthesis. PBPs are broadly classified as low molecular mass (LMM) and high molecular mass (HMM) based on their molecular weight. Although all PBPs share a set of highly conserved active site residues, different PBPs have different propensities for catalyzing reactions. To understand the structural differences among PBPs, a global catalytic residue comparison was performed for all the PBPs available in the protein data bank. This dataset was analyzed using univariate and multivariate statistical methods, revealing several interesting relationships such as: (1) Distribution of the dihedral angle for the SXXK-motif Lys side chain was bimodal, and strongly correlated with HMM/transpeptidase vs LMM/hydrolase activity; (2) Distance between the SXXK-motif Lys-NZ atom and the Lys/His-nitrogen atom of the (K/H)T(S)G-motif was highly conserved.