4UZ3

Crystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L endopeptidase from T. thermophilus bound to N-acetyl-chitohexaose

Summary for 4UZ3

• Entry DOI: 10.2210/pdb4uz3/pdb
• Related: 4UZ2 4XCM
• Descriptor: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (8 entities in total)
• Functional Keywords: hydrolase
• Biological source: THERMUS THERMOPHILUS
• Total number of polymer chains: 3
• Total formula weight: 37311.62

Authors

Wong, J.E.M.M.,Blaise, M. (deposition date: 2014-09-04, release date: 2015-01-14, Last modification date: 2024-05-08)

Primary citation

Wong, J.E.M.M.,Midtgaard, S.R.,Gysel, K.,Thygesen, M.B.,Sorensen, 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-, 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 (1.75 Å)