Module walking using an SH3‐like cell‐wall‐binding domain leads to a new GH184 family of muramidases

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2023-08, Vol.79 (8), p.706-720
• Main Authors: Moroz, Olga V., Blagova, Elena, Lebedev, Andrey A., Skov, Lars K., Pache, Roland A., Schnorr, Kirk M., Kiemer, Lars, Friis, Esben P., Nymand-Grarup, Søren, Ming, Li, Ye, Liu, Klausen, Mikkel, Cohn, Marianne T., Schmidt, Esben G. W., Davies, Gideon J., Wilson, Keith S.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Binding; Cell Wall; Cell walls; Fungi; GH184 family; Glycosidases; Glycoside hydrolase; glycoside hydrolase family 24; Glycoside Hydrolases - chemistry; Glycosides; lysins; lysozymes; Models, Molecular; module walking; Modules; Muramidase - chemistry; muramidases; Peptidoglycan; peptidoglycan cleavage; Peptidoglycans; Research Papers; Sequences; SH3‐like domains; Substrates; Trichophaea saccata
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798323005004

Muramidases (also known as lysozymes) hydrolyse the peptidoglycan component of the bacterial cell wall and are found in many glycoside hydrolase (GH) families. Similar to other glycoside hydrolases, muramidases sometimes have noncatalytic domains that facilitate their interaction with the substrate. Here, the identification, characterization and X‐ray structure of a novel fungal GH24 muramidase from Trichophaea saccata is first described, in which an SH3‐like cell‐wall‐binding domain (CWBD) was identified by structure comparison in addition to its catalytic domain. Further, a complex between a triglycine peptide and the CWBD from T. saccata is presented that shows a possible anchor point of the peptidoglycan on the CWBD. A `domain‐walking' approach, searching for other sequences with a domain of unknown function appended to the CWBD, was then used to identify a group of fungal muramidases that also contain homologous SH3‐like cell‐wall‐binding modules, the catalytic domains of which define a new GH family. The properties of some representative members of this family are described as well as X‐ray structures of the independent catalytic and SH3‐like domains of the Kionochaeta sp., Thermothielavioides terrestris and Penicillium virgatum enzymes. This work confirms the power of the module‐walking approach, extends the library of known GH families and adds a new noncatalytic module to the muramidase arsenal. The identification, characterization and X‐ray structure of a novel fungal GH24 muramidase from Trichophaea saccata is described in which an SH3‐like cell‐wall‐binding domain was identified by structure comparisons in addition to its catalytic domain. A domain‐walking approach was then used to identify a group of fungal muramidases that belong to a new GH family containing homologous SH3‐like cell‐wall‐binding modules, and X‐ray structures of the independent catalytic and SH3‐like domains of three of them are reported.