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Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases
Olga V Moroz1, Elena Blagova1, Andrey A Lebedev2
1York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
Abstract:
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.
Insights
Researchers discovered a new fungal muramidase (GH24) with a cell-wall-binding domain (CWBD). This finding expands the known glycoside hydrolase families and adds a novel noncatalytic module to the muramidase toolkit.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Muramidases (lysozymes) are glycoside hydrolases (GHs) that degrade bacterial peptidoglycan.
- Many GHs possess noncatalytic domains that enhance substrate interaction.
- Fungal muramidases represent a diverse group within the GH superfamily.
Purpose of the Study:
- To identify and characterize novel fungal muramidases.
- To elucidate the structure and function of a new GH24 muramidase from Trichophaea saccata.
- To explore the role of noncatalytic domains in fungal muramidase activity.
Main Methods:
- X-ray crystallography was employed to determine the structure of the T. saccata muramidase and its domains.
- Structure comparison and domain-walking approaches were used to identify homologous proteins.
- Biochemical characterization of representative fungal muramidase family members.
Main Results:
- A novel fungal GH24 muramidase from T. saccata was identified, featuring both catalytic and an SH3-like cell-wall-binding domain (CWBD).
- The crystal structure revealed a complex between the CWBD and a triglycine peptide, suggesting a peptidoglycan binding site.
- A new family of fungal muramidases containing homologous SH3-like CWBDs was discovered using a domain-walking strategy.
Conclusions:
- The study introduces a new fungal muramidase and a novel SH3-like CWBD, expanding the known repertoire of glycoside hydrolase families.
- The findings highlight the utility of structure-based domain analysis and domain-walking for discovering new enzyme families.
- This research provides insights into the structural basis of bacterial cell wall hydrolysis by fungal enzymes.
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