Folds and activities of peptidoglycan amidases

Abstract

Bacterial peptidoglycan amidases are a large and diverse group of enzymes. During the last few years, genomic sequence information has accumulated to an extent such that lists of proven or predicted peptidoglycan amidases can now be expected to be fairly complete. Moreover, representative crystal structures for most groups of phylogenetically related peptidoglycan amidases have been solved. Here, sequence and structural information is combined with published biochemical findings to demonstrate that (a) peptidoglycan amidases have evolved for almost every bond that occurs in peptidoglycan, (b) there are enzymes that share the fold, yet cleave different bonds and (c) there are enzymes that have entirely different folds and must have evolved independently, and yet cleave the same peptide bond. It is shown that despite these complications, some rules can be deduced from the available biochemical and structural information that can be useful to predict the specificity of hypothetical peptidoglycan hydrolases, for which only sequence information is available.

Activity of the Osmotically Regulated yqiHIK Promoter from Bacillus subtilis Is Controlled at a Distance

“…Our YqiI in silico model also highlights the position of residue E-148 (Fig. 3C), a residue that is critical for the biochemical functioning of N-acetylmuramoyl-Lalanine amidases (15,54). We note that apparently no cell wallbinding domain is present in the YqiI protein (Fig.…”

“…The analysis of the sequence of the 206 amino acids comprising the YqiI protein via the SMART Web tool (38) revealed the presence of a signal sequence (amino acids 1 to 23) for the Sec-mediated export of YqiI across the cytoplasmic membrane and an amidase_3 domain (from amino acids 67 to 178 of the mature protein), a domain which is found in many N-acetylmuramoyl-L-alanine amidases (15,55,62). This domain is present in the crystal structure of the catalytically active domain (CwlV1) of the cell wall hydrolase CwlV from Paenibacillus polymyxa var.…”

“…The predicted YqiI structure consists of a mixed ␤-sheet and five ␣-helices. This in silico model allowed the visualization of the positions of those residues (H-15, E-29, and H-82) that are known to be involved in coordinating the catalytically important zinc ion in N-acetylmuramoyl-L-alanine amidases (15), including that present in the CwlV enzyme (54), upon which the crystal structure of our YqiI in silico model is based. Our YqiI in silico model also highlights the position of residue E-148 (Fig.…”

“…Key to these processes is a situation-conform control of those hydrolytic enzymes, the autolysins, which hydrolyze various types of chemical bonds in the peptidoglycan superstructure (55,62) and therefore possess a potential cell-disruptive capability. Approximately 35 autolysins have been identified in B. subtilis and contribute to cell morphogenesis, motility, spore formation, and germination (15,55,62).…”

A highly coordinated cell wall degradation machine governs spore morphogenesis in Bacillus subtilis

“…To remodel this cell-shaped mesh, often referred to as the murein or PG sacculus, enzymes capable of breaking PG linkages are needed. Most bacteria encode a suite of these enzymes, and, in general, every amide and glycosidic linkage in PG is subject to cleavage by at least one family of enzymes that exists in nature (Firczuk and Bochtler 2007;Vollmer et al 2008).…”