Not classified in to the prior groups but which also function as
Not classified into the earlier groups but which also function as lysozymes/muramidases. The GO knowledgebase will be the world’s biggest source of facts on the functions of genes. In this work, the gene ontology for phage endolysin was analysed applying the QuickGo BMS-8 Technical Information web-site (http://www.ebi.ac.uk/QuickGO/, last accessed July 2021), which is a web-based tool that permits simple browsing on the Gene Ontology (GO) supplied by theMicroorganisms 2021, 9,15 ofGO Consortium annotation groups. Right here, we searched 3 specific GO terms: lysozyme, chitinase and endopeptidase (Supplementary Figure S4). The GO term GO:0003796 corresponds to lysozyme activity, whose ontology by molecular function describes this protein as “Catalysis of the hydrolysis on the beta-(1-4) linkages among N-acetylmuramic acid and N-acetyl-D-glucosamine residues within a peptidoglycan”. The GO term GO:0004568 corresponds to chitinase activity, whose ontology by molecular function describes this protein as “Catalysis from the hydrolysis of (1-4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins”. For each, all of the relationships inside the ancestor chart are “Is a”, such as the molecular function of hydrolase activity and peptidoglycan muralytic activity (Supplementary Figure S4a). The GO term GO:0004175 corresponds to endopeptidase activity, whose ontology by molecular function describes this protein as “Catalysis in the hydrolysis of internal, alpha-peptide bonds within a polypeptide chain”. For each lysozyme activity (GO:0003796) and chitinase activity (GO:0004568), each of the relationships within the Ancestor Chart are “Is a”, such as the molecular function of hydrolase activity and peptidoglycan muralytic activity (Supplementary Figure S4b). For endopeptidase activity (GO:0004175), the majority of the relationships are “Is a”, such as the molecular function of peptidase activity and catalytic activity, acting on a protein and hydrolase activity; however it is also probable to see a single “Part of”, showing the biological course of action of proteolysis (Supplementary Figure S4c). Joining previous analysis, structural homology and GO terms searched, endolysins were attributed to three common classes: lysozyme/muramidases (n = 99), glycosidases/ chitinases (n = 31) and endopeptidases (n = 2). The lysozyme and chitinase classes have been identified in all K. pneumoniae prophages described here, whereas the two endopeptidases had been identified in two related phages (Klebsiella phages ST846-OXA48phi9.1 and 48ST307; GenBank: MK416021.1 and KY271402.1, respectively). Though endolysins integrated into Group 1 have various nucleotides and amino acid sequences, they fall into the very same class. All of them are lysozymes/muramidases and can hydrolyse -1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan at the same time as inside N-acetyl-D-glucosamine residues. Within the case with the chitinases (Group 4), the enzyme binds to chitin and randomly cleaves glycosidic linkages in chitin and chitodextrins in a non-processive mode, creating chitooligosaccharides and totally free ends on which exo-chitinases and exo-chitodextrinases can act [70]. Remarkably, Group 6 includes a single endopeptidase identified from Klebsiella phage ST846-OXA48phi9.1 (GenBank: MK416021), which share a greater identity (higher than 80 ) with endolysin R21 like-proteins despite their diverse function. The endolysins identified here had a predicted molecular weight involving 16.06 and 24.31 kDa, Scaffold Library MedChemExpress consistent.
