8B2G

SH3-like domain from Penicillium virgatum muramidase

Summary for 8B2G

• Entry DOI: 10.2210/pdb8b2g/pdb
• Descriptor: SH3b domain-containing protein, 1,2-ETHANEDIOL, ZINC ION, ... (4 entities in total)
• Functional Keywords: sh3-like, muramidase, peptidoglycan, cell wall binding domain, hydrolase
• Biological source: Penicillium virgatum
• Total number of polymer chains: 2
• Total formula weight: 15896.77

Authors

Moroz, O.V.,Blagova, E.,Lebedev, A.A.,Skov, L.K.,Pache, R.A.,Schnorr, K.M.,Kiemer, L.,Nymand-Grarup, S.,Ming, L.,Ye, L.,Klausen, M.,Cohn, M.T.,Schmidt, E.G.W.,Davies, G.J.,Wilson, K.S. (deposition date: 2022-09-13, release date: 2023-07-19, Last modification date: 2024-11-13)

Primary citation

Moroz, O.V.,Blagova, E.,Lebedev, A.A.,Skov, L.K.,Pache, R.A.,Schnorr, K.M.,Kiemer, L.,Friis, E.P.,Nymand-Grarup, S.,Ming, L.,Ye, L.,Klausen, M.,Cohn, M.T.,Schmidt, E.G.W.,Davies, G.J.,Wilson, K.S.
Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.
Acta Crystallogr D Struct Biol, 79:706-720, 2023

PubMed 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.

PubMed: 37428847
DOI: 10.1107/S2059798323005004

Experimental method

X-RAY DIFFRACTION (1.5 Å)