4XCM

Crystal structure of the putative NlpC/P60 D,L endopeptidase from T. thermophilus

Summary for 4XCM

• Entry DOI: 10.2210/pdb4xcm/pdb
• Descriptor: Cell wall-binding endopeptidase-related protein (2 entities in total)
• Functional Keywords: nlpc/p60, d, l-endopeptidase, lysm domain, hydrolase
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 2
• Total formula weight: 53379.93

Authors

Wong, J.,Midtgaard, S.,Gysel, K.,Thygesen, M.B.,Sorensen, K.K.,Jensen, K.J.,Stougaard, J.,Thirup, S.,Blaise, M. (deposition date: 2014-12-18, release date: 2015-01-14, Last modification date: 2024-10-23)

Primary citation

Wong, J.E.,Midtgaard, S.R.,Gysel, K.,Thygesen, M.B.,Srensen, K.K.,Jensen, K.J.,Stougaard, J.,Thirup, S.,Blaise, M.
An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase.
Acta Crystallogr.,Sect.D, 71:592-605, 2015

PubMed Abstract: LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.

PubMed: 25760608
DOI: 10.1107/S139900471402793X

Experimental method

X-RAY DIFFRACTION (2.65 Å)