cereus ATCC 10876, as described previously (Kuroda & Sekiguchi, 1990), and incubated Protein Tyrosine Kinase inhibitor with 5 μg LysBPS13 at 25 °C for 30 min. N-acetylmuramyl-l-alanine amidase activity was measured as described previously (Hadzija, 1974; Hazenberg & de Visser, 1992). Briefly, muramic acid was degraded to lactic acid by N-acetylmuramyl-l-alanine amidases, and the lactic acid product was degraded to acetaldehyde, which was determined colorimetrically with p-hydroxydiphenyl (PHD).
Muramic acid was used as the standard. Glycosidase activity was assayed by quantifying the released reducing sugars from the extracted peptidoglycan, according to Pritchard et al. (2004). A putative endolysin gene was identified in the genome of the bacteriophage BPS13, which infects B. cereus (H Shin, J Park, and S Ryu, unpublished data). According to blastp analysis (Marchler-Bauer et al., 2011), an 834-bp-long ORF (locus tag 0008) showed high similarity to the N-acetylmuramyl-l-alanine amidase of Bacillus phage TP21-L (CAA72267.1, E-value = 2 × 10−110) and other amidases of Bacillus strains and Bacillus-infecting bacteriophages (ZP_03236042, E-value = 2 × 10−76; YP_002154393,
E-value = 6 × 10−74). However, this ORF, termed lysBPS13, was not similar to the well-characterized N-acetylmuramyl-l-alanine amidases, such as PlyCA (AAP42310.2), Ply511 (CAA59368.1), T7 lysozyme (AAB32819.1), and PlyL (YP_002868169.1). Searching for VX-809 molecular weight conserved domains in the Conserved Domain Database (Marchler-Bauer et al., 2011) revealed that LysBPS13 consisted of an N-terminal catalytic domain and a C-terminal cell wall binding domain, similar to most endolysins from bacteriophages that infect Gram-positive bacteria (Fischetti, 2008) (Fig. 1a). The predicted N-terminal catalytic domain was the peptidoglycan recognition protein (PGRP; cd06583, E-value = 2.19 × 10−19). Methocarbamol As a subset of the PGRP family binds zinc (Zn2+), which is coordinated by two His residues and a Cys or Asp residue (Cheng et al., 1994; Dziarski & Gupta, 2006), LysBPS13 was found to contain the conserved
motif of three zinc-binding residues (His29, His129, and Cys137) (Fig. 1a). This N-terminal catalytic domain was found in many N-acetylmuramyl-l-alanine amidases of Bacillus phages or Bacillus species and even in the genomes of many vertebrates (Dziarski & Gupta, 2006). In mammals, some PGRPs belong to N-acetylmuramyl-l-alanine amidases, which are involved in reducing proinflammatory acidity or in killing bacteria (Dziarski, 2004; Vollmer et al., 2008). Among endolysins, PGRP domains correspond to catalytic domains of amidases such as Ply21 and mycobacteriophage Ms6 LysA (Loessner et al., 1997; Catalao et al., 2011). However, the PGRP domain was not well characterized with regard to peptidoglycan degradation, unlike the CHAP domain (PF05257) of other N-acetylmuramyl-l-alanine amidases such as PlyC and LytA (P24556) (Bateman & Rawlings, 2003; Nelson et al., 2006).