PMID:18560152

Citation	Korndörfer, IP, Kanitz, A, Danzer, J, Zimmer, M, Loessner, MJ and Skerra, A (2008) Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family. Acta Crystallogr. D Biol. Crystallogr. 64:644-50
Abstract	Similar to many other bacterial cell-wall-hydrolyzing enzymes, the Listeria bacteriophage A500 endopeptidase Ply500 has a modular architecture consisting of an enzymatically active domain (EAD) linked to a cell-wall-binding domain (CBD) in a single polypeptide chain. The crystal structure of the EAD of Ply500 has been solved at 1.8 A resolution. The shape of the enzyme resembles a sofa chair: one alpha-helix and three antiparallel beta-strands form the seat, which is supported by two more alpha-helices, while another alpha-helix together with the following loop give rise to the backrest. A sulfate anion bound to the active site, which harbours a catalytic Zn2+ ion, indicates mechanistic details of the peptidase reaction, which involves a tetrahedral transition state. Despite very low sequence similarity, a clear structural relationship was detected to the peptidases VanX, DDC, MSH and MepA, which belong to the so-called 'LAS' family. Their gross functional similarity is supported by a common bound Zn2+ ion and a highly conserved set of coordinating residues (His80, Asp87 and His133) as well as other side chains (Arg50, Gln55, Ser78 and Asp130) in the active site. Considering the high sequence similarity to the EAD of the Listeria phage endopeptidase Ply118, both enzymes can thus be assigned to the LAS family. The same is the case for the L,D-endopeptidase CwlK from Bacillus subtilis, which shows both functional and amino-acid sequence similarity. The fact that the CBD of Ply500 is closely homologous to the CBD of the Listeria phage N-acetylmuramoyl-L-alanine amidase PlyPSA, which exhibits a totally different EAD, illustrates the modular composition and functional variability of this class of enzymes and opens interesting possibilities for protein engineering.
Links	PubMed Online version:10.1107/S0907444908007890
Keywords	Amino Acid Sequence; Bacteriophages/enzymology; Bacteriophages/genetics; Base Sequence; Catalytic Domain; Crystallography, X-Ray; DNA Primers/genetics; DNA, Viral/genetics; Endopeptidases/chemistry; Endopeptidases/genetics; Listeria monocytogenes/virology; Models, Molecular; Molecular Sequence Data; Protein Structure, Tertiary; Recombinant Proteins/chemistry; Recombinant Proteins/genetics; Sequence Homology, Amino Acid
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BPA50:AEPE	Contributes to	GO:0016787: hydrolase activity	ECO:0000247:	UniProtKB:Q37976	F		The N-terminal enzymatically active domain (EAD) of an endolysin is the source of it's catalytic behavior, and in this sense, will determine evidence of hydrolytic activity. Endolysin PLY500 has displayed L-alanoyl-D-glutamate endopeptidase activity in Listeria phages. Listeria phage PLY118 (Listeria phage A118) shows 30% amino acid alignment with PLY500 in terms of EAD (fig.1, indicated by overhead black bars). While there is no relations between the C-terminal domains (structural evidence) of PLY500 and PLY118, the genes active in binding the catalytic Zn2+ ion and LAS protein identification are conserved within this 30% PLY118 matching amino acid sequence. From this information it is likely that the N-terminal domains of PLY118 and PLY500 are similar enough to be classified in the same functional LAS family.	complete CACAO 12475
BPA50:AEPE		GO:0071555: cell wall organization	ECO:0000314:		P		Figure 1 of the paper compares proteins PLY500 and PLY118. According to the introduction of the paper PLY500 is an endolysin that consists of a C-terminal cell wall binding domain and a N-terminal enzymatically active domain (EAD). The cell wall binding domain is for recognizing and binding to specific bacterial cell surfaces. PLY118 is another protein from a related Listeria phage, A118. PLY118 is a peptidase in A118. Both of these proteins have unrelated cell wall binding domains but their endopeptidase has a clear sequence homology to EAD500. EAD500 was recently shown to be chromosomally encoded in Bacillus subtilis.	complete CACAO 12635

References

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