An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

Mei Mei Jaslyn Elizabeth Wong; Søren Roi Midtgaard; Kira Gysel; Mikkel Boas Thygesen; Kasper Kildegaard Sørensen; Knud Jørgen Jensen; Jens Stougaard; Søren Skou Thirup; Mickael Blaise

doi:10.1107/S139900471402793X

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

Mei Mei Jaslyn Elizabeth Wong, Søren Roi Midtgaard, Kira Gysel, Mikkel Boas Thygesen, Kasper Kildegaard Sørensen, Knud Jørgen Jensen, Jens Stougaard, Søren Skou Thirup, Mickael Blaise

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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.

Original language	English
Journal	Acta Crystallographica. Section D: Biological Crystallography
Volume	71
Pages (from-to)	592-605
Number of pages	14
ISSN	0907-4449
DOIs	https://doi.org/10.1107/S139900471402793X
Publication status	Published - 1 Mar 2015

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An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidaseFinal published version, 2.83 MBLicence: CC BY

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Wong, M. M. J. E., Midtgaard, S. R., Gysel, K., Thygesen, M. B., Sørensen, K. K., Jensen, K. J., Stougaard, J., Thirup, S. S., & Blaise, M. (2015). An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase. Acta Crystallographica. Section D: Biological Crystallography, 71, 592-605. https://doi.org/10.1107/S139900471402793X

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase. / Wong, Mei Mei Jaslyn Elizabeth; Midtgaard, Søren Roi; Gysel, Kira et al.

In: Acta Crystallographica. Section D: Biological Crystallography, Vol. 71, 01.03.2015, p. 592-605.

Research output: Contribution to journal › Journal article › Research › peer-review

Wong, MMJE, Midtgaard, SR, Gysel, K, Thygesen, MB, Sørensen, KK, Jensen, KJ, Stougaard, J, Thirup, SS & Blaise, M 2015, 'An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase', Acta Crystallographica. Section D: Biological Crystallography, vol. 71, pp. 592-605. https://doi.org/10.1107/S139900471402793X

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title = "An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase",

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.",

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AU - Wong, Mei Mei Jaslyn Elizabeth

AU - Midtgaard, Søren Roi

AU - Gysel, Kira

AU - Thygesen, Mikkel Boas

AU - Sørensen, Kasper Kildegaard

AU - Jensen, Knud Jørgen

AU - Stougaard, Jens

AU - Thirup, Søren Skou

AU - Blaise, Mickael

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N2 - 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.

AB - 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.

U2 - 10.1107/S139900471402793X

DO - 10.1107/S139900471402793X

M3 - Journal article

C2 - 25760608

SN - 2059-7983

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SP - 592

EP - 605

JO - Acta Crystallographica Section D: Structural Biology

JF - Acta Crystallographica Section D: Structural Biology

ER -

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

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