PeiW (UniProtKB Q7LYX0) and PeiP (UniProtKB Q77WJ4) are the two major pseudomurein endoisopeptidases (Pei) that are known to cleave pseudomurein cell-wall sacculi of the members of the methanogenic orders Methanobacteriales and Methanopyrales. Both enzymes, originating from prophages specific for some methanogenic archaeal species, hydrolyze the (Ala)-Lys bond of the peptide linker between adjacent pseudomurein layers. Because lysozyme is not able to cleave the pseudomurein cell wall, the enzymes are used in protoplast preparation and in DNA isolation from pseudomurein cell-wall-containing methanogens. Moreover, PeiW increases the probe permeability ratio and enables fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-) FISH experiments to be performed on these methanogens. 1. Introduction Bacterial peptidoglycan hydrolases are among the most extensively studied hydrolases. Many three-dimensional structures of murein hydrolases have already been deposited in the Protein Data Bank; on the other hand, pseudomurein hydrolases are very poorly studied. Pseudomurein, the major cell wall component of gram-positive methanogenic archaea, is composed of -acetyl-D-glucosamine (NAG) and -acetyl-L-talosaminuronic acid (NAT) linked by a -glycosidic bond (see Figure 1) [1, 2]. Therefore, it is resistant to lysozyme and other bacterial hydrolases. The other cell wall polymers of methanogens include methanochondroitin and (glyco)protein surface (S)-layers [3]. Not much is known with regard to cell-wall-degrading lysins in methanogenic archaea. Pseudomurein endoisopeptidase (Pei) is the first enzyme known to hydrolyze the pseudomurein sacculi of archaeal methanogens [2, 4–7]. Figure 1: Dimer structure of pseudomurein and cleavage sites of pseudomurein endoisopeptidase (Pei). Block arrows indicate the cleavage site of Pei in the peptide subunit. The picture was adapted and modified from Kiener et al. [ 4]. This short review not only gathers the available data on this unique enzyme but also enlightens its future research prospective. There is no three-dimensional structure of this enzyme despite its novelty and application potential. Further, research leading to the elucidation of the three-dimensional structure of pseudomurein endoisopeptidase may substantially increase our knowledge of its functionalities and possible applications to commercially and environmentally important methanogens. 2. The Pei Enzyme Pseudomurein endoisopeptidase belongs to peptidase family C71, which contains peptidases that cleave the peptide subunits of pseudomurein
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