Is the LysM domain ofL. monocytogenesp60 protein suitable for engineering a protein with high peptidoglycan binding affinity?

Abstract

Lysin motif (LysM) is a highly conserved carbohydrate binding module that is widely present in proteins from both prokaryotes and eukaryotes. LysM domains from many LysM-containing proteins can be taken out of their natural context and retain their ability to bind peptidoglycan. Therefore, LysM has enormous potential for applications in both industry and medicine. This potential has stimulated an intensive search for LysM modules with different evolutionary origins. The p60 protein (Lm-p60) is an NlpC/P60-containing peptidoglycan hydrolase secreted by Listeria monocytogenes. The N-terminus of Lm-p60 contains 2 LysM modules separated by an SH3 module. Our recent study of Lm-p60 demonstrates that the N-terminal half of Lm-p60, comprised of 2 LysM and 1 SH3 module, is able to recognize and bind peptidoglycan. The LysM domain of Lm-p60 contains only 2 LysM modules, which is the minimum number of LysM modules in most NlpC/P60-containing proteins, but it shows strong affinity for peptidoglycan. Moreover, these 2 LysM modules have only 38.64% similarity to each other. These data allowed us to conclude that the 2 LysM modules from Lm-p60 have different evolutionary origins, suggesting that they are suitable candidate peptidoglycan-binding modules for protein engineering in order to create a protein with a high binding affinity to peptidoglycan.

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan

“…These two latter enzyme families contain a circularly permuted catalytic domain where the relative positions of the cysteine and histidine/polar residue of the conserved catalytic triad are swapped in the primary sequence (Anantharaman and Aravind, 2003). In B. subtilis , LytF and LytE, which belong to the P60-like family, break the linkage of m-diaminopimelic acid of the PG (Yu et al, 2016). Structure determination of NlpC/P60 domain in CwlT from Clostridioides difficile , previously known as Clostridium difficile or Peptoclostridium difficile (Yutin and Galperin, 2013; Lawson et al, 2016), revealed a conserved Cys-His-His-Tyr active site specific to tetrapeptide (Xu et al, 2014).…”

Antigenic sites in SARS-CoV-2 spike RBD show molecular similarity with pathogenic antigenic determinants and harbors peptides for vaccine development

“…The30kDa urease subunit alpha (ureA) from Helicobacter pylori acts as virulence factor and cause infection in stomach via host-pathogen interaction ( Schoep et al, 2010 ) and mediate immune response in humans ( Schoep et al, 2010 ). The endopeptidase p60 (Lm-p60) of Listeria monocytogenes whose sequence was also predicted in similar search is a highly conserved carbohydrate binding module which can be engineered for binding to peptidoglycans with high affinity ( Yu et al, 2016 ). Mycobacterium leprae has two proteins (ESAT-6 like protein esxb and 10 kDa chaperonin groS) that showed molecular similarity with predicted antigens in SARS-CoV-2 RBD.…”

Direct interaction between marine cyanobacteria mediated by nanotubes

“…The peptidoglycan endopeptidase LytE breaks the linkage of m -diaminopimelic acid of the peptidoglycan ( 66 ), and putative homologs are present in marine Prochlorococcus and Synechococcus (tables S3 to S5). In contrast, YmdB protein, which was shown to be important for nanotube formation in B. subtilis ( 8 ), was not found in picocyanobacteria.…”