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Laguri C, Sadir R, Gout E, Vivès RR, Lortat-Jacob H. Preparation and Characterization of Heparan Sulfate-Derived Oligosaccharides to Investigate Protein-GAG Interaction and HS Biosynthesis Enzyme Activity. Methods Mol Biol 2022; 2303:121-137. [PMID: 34626375 DOI: 10.1007/978-1-0716-1398-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Heparan sulfate chains are complex and structurally diverse polysaccharides that interact with a large number of proteins, thereby regulating a vast array of biological functions. Understanding this activity requires obtaining oligosaccharides of defined structures. Here we describe methods for isolating, engineering, and characterizing heparan sulfate-derived oligosaccharides and approaches based on high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR), and bio-layer interferometry (BLI) to study their structures, modifications, and interactions.
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Affiliation(s)
- Cédric Laguri
- Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, UMR 5075, Grenoble, France
| | - Rabia Sadir
- Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, UMR 5075, Grenoble, France
| | - Evelyne Gout
- Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, UMR 5075, Grenoble, France
| | - Romain R Vivès
- Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, UMR 5075, Grenoble, France
| | - Hugues Lortat-Jacob
- Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, UMR 5075, Grenoble, France.
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2
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Préchoux A, Simorre JP, Lortat-Jacob H, Laguri C. Deciphering the structural attributes of protein-heparan sulfate interactions using chemo-enzymatic approaches and NMR spectroscopy. Glycobiology 2021; 31:851-858. [PMID: 33554262 DOI: 10.1093/glycob/cwab012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/18/2020] [Accepted: 01/28/2021] [Indexed: 11/14/2022] Open
Abstract
Heparan sulfates (HS) is a polysaccharide found at the cell surface, where it mediates interactions with hundreds of proteins and regulates major pathophysiological processes. HS is highly heterogeneous and structurally complex and examples that define their structure-activity relationships remain limited. Here, to characterize a protein-HS interface and define the corresponding saccharide binding domain, we present a chemoenzymatic approach that generate 13C labeled HS-based oligosaccharide structures. NMR spectroscopy that efficiently discriminates between important or redundant chemical groups in the oligosaccharides, is employed to characterize these molecules alone and in interaction with proteins. Using chemokines as model system, docking based on NMR data on both proteins and oligosaccharides enable the identification of the structural determinant involved in the complex. This study shows that both the position of the sulfo-groups along the chain and their mode of presentation, rather than their overall number, are key determinant and further points out the usefulness of these 13C labeled oligosaccharides in obtaining detailed structural information on HS-protein complexes.
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Affiliation(s)
| | | | | | - Cédric Laguri
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble
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3
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Dekoninck K, Létoquart J, Laguri C, Demange P, Bevernaegie R, Simorre JP, Dehu O, Iorga BI, Elias B, Cho SH, Collet JF. Defining the function of OmpA in the Rcs stress response. eLife 2020; 9:60861. [PMID: 32985973 PMCID: PMC7553776 DOI: 10.7554/elife.60861] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/26/2020] [Indexed: 01/18/2023] Open
Abstract
OmpA, a protein commonly found in the outer membrane of Gram-negative bacteria, has served as a paradigm for the study of β-barrel proteins for several decades. In Escherichia coli, OmpA was previously reported to form complexes with RcsF, a surface-exposed lipoprotein that triggers the Rcs stress response when damage occurs in the outer membrane and the peptidoglycan. How OmpA interacts with RcsF and whether this interaction allows RcsF to reach the surface has remained unclear. Here, we integrated in vivo and in vitro approaches to establish that RcsF interacts with the C-terminal, periplasmic domain of OmpA, not with the N-terminal β-barrel, thus implying that RcsF does not reach the bacterial surface via OmpA. Our results suggest a novel function for OmpA in the cell envelope: OmpA competes with the inner membrane protein IgaA, the downstream Rcs component, for RcsF binding across the periplasm, thereby regulating the Rcs response.
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Affiliation(s)
- Kilian Dekoninck
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Juliette Létoquart
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | | | - Pascal Demange
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Robin Bevernaegie
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Olivia Dehu
- de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Bogdan I Iorga
- de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium.,Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Seung-Hyun Cho
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Jean-Francois Collet
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
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Caveney NA, Egan AJF, Ayala I, Laguri C, Robb CS, Breukink E, Vollmer W, Strynadka NCJ, Simorre JP. Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa. Structure 2020; 28:643-650.e5. [PMID: 32320673 PMCID: PMC7267771 DOI: 10.1016/j.str.2020.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/15/2020] [Accepted: 03/24/2020] [Indexed: 12/23/2022]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall and is assembled from a lipid II precursor by glycosyltransferase and transpeptidase reactions catalyzed in particular by bifunctional class A penicillin-binding proteins (aPBPs). In the major clinical pathogen Pseudomonas aeruginosa, PBP1B is anchored within the cytoplasmic membrane but regulated by a bespoke outer membrane-localized lipoprotein known as LpoP. Here, we report the structure of LpoP, showing an extended N-terminal, flexible tether followed by a well-ordered C-terminal tandem-tetratricopeptide repeat domain. We show that LpoP stimulates both PBP1B transpeptidase and glycosyltransferase activities in vitro and interacts directly via its C terminus globular domain with the central UB2H domain of PBP1B. Contrary to the situation in E. coli, P. aeruginosa CpoB does not regulate PBP1B/LpoP in vitro. We propose a mechanism that helps to underscore similarities and differences in class A PBP activation across Gram-negative bacteria. Structural organization of LpoP has been resolved PaPBP1B is directly stimulated by LpoP but not by PaCpoB in vitro LpoP likely interacts between the GTase and UB2H domains of PaPBP1B
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Affiliation(s)
- Nathanael A Caveney
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada
| | - Alexander J F Egan
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Isabel Ayala
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Cédric Laguri
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada.
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5
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Maya-Martinez R, Alexander JAN, Otten CF, Ayala I, Vollmer D, Gray J, Bougault CM, Burt A, Laguri C, Fonvielle M, Arthur M, Strynadka NCJ, Vollmer W, Simorre JP. Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus. Front Microbiol 2019; 9:3223. [PMID: 30713527 PMCID: PMC6346638 DOI: 10.3389/fmicb.2018.03223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan (PG) is an essential component of the cell envelope, maintaining bacterial cell shape and protecting it from bursting due to turgor pressure. The monoderm bacterium Staphylococcus aureus has a highly cross-linked PG, with ~90% of peptide stems participating in DD-cross-links and up to 15 peptide stems connected with each other. These cross-links are formed in transpeptidation reactions catalyzed by penicillin-binding proteins (PBPs) of classes A and B. Most S. aureus strains have three housekeeping PBPs with this function (PBP1, PBP2, and PBP3) but MRSA strains have acquired a third class B PBP, PBP2a, which is encoded by the mecA gene and required for the expression of high-level resistance to β-lactams. Another housekeeping PBP of S. aureus is PBP4, which belongs to the class C PBPs, and hence would be expected to have PG hydrolase (DD-carboxypeptidase or DD-endopeptidase) activity. However, previous works showed that, unexpectedly, PBP4 has transpeptidase activity that significantly contributes to both the high level of cross-linking in the PG of S. aureus and to the low level of β-lactam resistance in the absence of PBP2a. To gain insights into this unusual activity of PBP4, we studied by NMR spectroscopy its interaction in vitro with different substrates, including intact peptidoglycan, synthetic peptide stems, muropeptides, and long glycan chains with uncross-linked peptide stems. PBP4 showed no affinity for the complex, intact peptidoglycan or the smallest isolated peptide stems. Transpeptidase activity of PBP4 was verified with the disaccharide peptide subunits (muropeptides) in vitro, producing cyclic dimer and multimer products; these assays also showed a designed PBP4(S75C) nucleophile mutant to be inactive. Using this inactive but structurally highly similar variant, liquid-state NMR identified two interaction surfaces in close proximity to the central nucleophile position that can accommodate the potential donor and acceptor stems for the transpeptidation reaction. A PBP4:muropeptide model structure was built from these experimental restraints, which provides new mechanistic insights into mecA independent resistance to β-lactams in S. aureus.
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Affiliation(s)
| | - J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Isabel Ayala
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daniela Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Alister Burt
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Cédric Laguri
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Matthieu Fonvielle
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Connell BJ, Sadir R, Baleux F, Laguri C, Kleman JP, Luo L, Arenzana-Seisdedos F, Lortat-Jacob H. Heparan sulfate differentially controls CXCL12α- and CXCL12γ-mediated cell migration through differential presentation to their receptor CXCR4. Sci Signal 2016; 9:ra107. [PMID: 27803285 DOI: 10.1126/scisignal.aaf1839] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemokines stimulate signals in cells by binding to G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors. These chemoattractant cytokines also interact with heparan sulfate (HS), which provides positional information within tissues in the form of haptotactic gradients along which cells can migrate directionally. To investigate the mechanism by which HS modulates chemokine functions, we used the CXC chemokine CXCL12, which exists in different isoforms that all signal through CXCR4 but have distinct HS-binding domains. In experiments with both cell-associated and solubilized CXCR4, we found that although CXCL12γ bound to CXCR4 with a higher affinity than did CXCL12α, CXCL12γ displayed reduced signaling and chemotactic activities. These properties were caused by the specific carboxyl-terminal region of CXCL12γ, which, by interacting with CXCR4 sulfotyrosines, mediated high-affinity, but nonproductive, binding to CXCR4. HS prevented CXCL12γ from interacting with the CXCR4 sulfotyrosines, thereby functionally presenting the chemokine to its receptor such that its activity was similar to that of CXCL12α. HS had no effects on the binding of CXCL12α to CXCR4 or its biological activity, suggesting that this polysaccharide controls CXCL12 in an isoform-specific manner. These data suggest that the HS-dependent regulation of chemokine functions extends beyond the simple process of immobilization and directly modulates receptor ligation and activation.
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Affiliation(s)
- Bridgette J Connell
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, F-38027 Grenoble, France
| | - Rabia Sadir
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, F-38027 Grenoble, France
| | - Françoise Baleux
- Institut Pasteur, Unité de Chimie des Biomolécules, UMR CNRS 3523, Paris, France
| | - Cédric Laguri
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, F-38027 Grenoble, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, F-38027 Grenoble, France
| | - Lingjie Luo
- Institut Pasteur, INSERM U1108, Paris, France
| | | | - Hugues Lortat-Jacob
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, F-38027 Grenoble, France.
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7
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Triboulet S, Bougault CM, Laguri C, Hugonnet JE, Arthur M, Simorre JP. Acyl acceptor recognition by Enterococcus faecium L,D-transpeptidase Ldtfm. Mol Microbiol 2015; 98:90-100. [PMID: 26101813 DOI: 10.1111/mmi.13104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 11/27/2022]
Abstract
In Mycobacterium tuberculosis and ampicillin-resistant mutants of Enterococcus faecium, the classical target of β-lactam antibiotics is bypassed by L,D-transpeptidases that form unusual 3 → 3 peptidoglycan cross-links. β-lactams of the carbapenem class, such as ertapenem, are mimics of the acyl donor substrate and inactivate l,d-transpeptidases by acylation of their catalytic cysteine. We have blocked the acyl donor site of E. faecium L,D-transpeptidase Ldt(fm) by ertapenem and identified the acyl acceptor site based on analyses of chemical shift perturbations induced by binding of peptidoglycan fragments to the resulting acylenzyme. An nuclear magnetic resonance (NMR)-driven docking structure of the complex revealed key hydrogen interactions between the acyl acceptor and Ldt(fm) that were evaluated by site-directed mutagenesis and development of a cross-linking assay. Three residues are reported as critical for stabilisation of the acceptor in the Ldt(fm) active site and proper orientation of the nucleophilic nitrogen for the attack of the acylenzyme carbonyl. Identification of the catalytic pocket dedicated to the acceptor substrate opens new perspectives for the design of inhibitors with an original mode of action that could act alone or in synergy with β-lactams.
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Affiliation(s)
- Sébastien Triboulet
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Equipe 12, F-75006, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France
| | - Catherine M Bougault
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Cédric Laguri
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Jean-Emmanuel Hugonnet
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Equipe 12, F-75006, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France
| | - Michel Arthur
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Equipe 12, F-75006, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, F-75006, Paris, France
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
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8
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Préchoux A, Halimi C, Simorre JP, Lortat-Jacob H, Laguri C. C5-epimerase and 2-O-sulfotransferase associate in vitro to generate contiguous epimerized and 2-O-sulfated heparan sulfate domains. ACS Chem Biol 2015; 10:1064-71. [PMID: 25594747 DOI: 10.1021/cb501037a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heparan sulfate (HS), a complex polysaccharide of the cell surface, is endowed with the remarkable ability to bind numerous proteins and, as such, regulates a large variety of biological processes. Protein binding depends on HS structure; however, in the absence of a template driving its biosynthesis, the mechanism by which protein binding sequences are assembled remains poorly known. Here, we developed a chemically defined 13C-labeled substrate and NMR based experiments to simultaneously follow in real time the activity of HS biosynthetic enzymes and characterize the reaction products. Using this new approach, we report that the association of C5-epimerase and 2-O-sulfotransferase, which catalyze the production of iduronic acid and its 2-O-sulfation, respectively, is necessary to processively generate extended sequences of contiguous IdoA2S-containing disaccharides, whereas modifications are randomly introduced when the enzymes are uncoupled. These data shed light on the mechanisms by which HS motifs are generated during biosynthesis. They support the view that HS structure assembly is controlled not only by the availability of the biosynthetic enzymes but also by their physical association, which in the case of the C5-epimerase and 2-O-sulfotransferase was characterized by an affinity of 80 nM as demonstrated by surface plasmon resonance experiments.
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Affiliation(s)
- Aurélie Préchoux
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Célia Halimi
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Hugues Lortat-Jacob
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Cédric Laguri
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
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9
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Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre JP. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. J Am Chem Soc 2014; 136:17852-60. [PMID: 25429710 PMCID: PMC4544747 DOI: 10.1021/ja5105987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
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Affiliation(s)
- Paul Schanda
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Sébastien Triboulet
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Cédric Laguri
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Catherine M. Bougault
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Morgane Callon
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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10
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Saesen E, Sarrazin S, Laguri C, Sadir R, Maurin D, Thomas A, Imberty A, Lortat-Jacob H. Insights into the mechanism by which interferon-γ basic amino acid clusters mediate protein binding to heparan sulfate. J Am Chem Soc 2013; 135:9384-90. [PMID: 23734709 DOI: 10.1021/ja4000867] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The extensive functional repertoire of heparin and heparan sulfate, which relies on their ability to interact with a large number of proteins, has recently emerged. To understand the forces that drive such interactions the binding of heparin to interferon-γ (IFNγ), used as a model system, was investigated. NMR-based titration experiments demonstrated the involvement of two adjacent cationic domains (D1: KTGKRKR and D2: RGRR), both of which are present within the carboxy-terminal sequence of the cytokine. Kinetic analysis showed that these two domains contribute differently to the interaction: D1 is required to form a complex and constitutes the actual binding site, whereas D2, although unable to associate with heparin by itself, increased the association rate of the binding. These data are consistent with the view that D2, through nonspecific electrostatic forces, places the two molecules in favorable orientations for productive binding within the encounter complex. This mechanism was supported by electrostatic potential analysis and thermodynamic investigations. They showed that D1 association to heparin is driven by both favorable enthalpic and entropic contributions, as expected for a binding sequence, but that D2 gives rise to entropic penalty, which opposes binding in a thermodynamic sense. The binding mechanism described herein, by which the D2 domain kinetically drives the interaction, has important functional consequences and gives a structural framework to better understand how specific are the interactions between proteins and heparin.
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Affiliation(s)
- Els Saesen
- Institut de Biologie Structurale, CNRS, CEA, University Grenoble Alpes, UMR 5075, 41 rue Horowitz, 38027, Grenoble cedex 01, France
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11
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Seffouh A, Milz F, Przybylski C, Laguri C, Oosterhof A, Bourcier S, Sadir R, Dutkowski E, Daniel R, van Kuppevelt TH, Dierks T, Lortat-Jacob H, Vivès RR. HSulf sulfatases catalyze processive and oriented 6-O-desulfation of heparan sulfate that differentially regulates fibroblast growth factor activity. FASEB J 2013; 27:2431-9. [PMID: 23457216 DOI: 10.1096/fj.12-226373] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sulfs are extracellular sulfatases that have emerged recently as critical regulators of heparan sulfate (HS) activities through their ability to catalyze specific 6-O-desulfation of the polysaccharide. Consequently, Sulfs have been involved in many physiological and pathological processes, and notably for Sulf-2, in the development of cancers with poor prognosis. Despite growing interest, little is known about the structure and activity of these enzymes and the way they induce dynamic remodeling of HS 6-O-sulfation status. Here, we have combined an array of analytical approaches, including mass spectrometry, NMR, HS oligosaccharide sequencing, and FACS, to dissect HSulf-2 sulfatase activity, either on a purified octasaccharide used as a mimic of HS functional domains, or on intact cell-surface HS chains. In parallel, we have studied the functional consequences of HSulf-2 activity on fibroblast growth factor (FGF)-induced mitogenesis and found that the enzyme could differentially regulate FGF1 and FGF2 activities. Notably, these data supported the existence of precise 6-O-sulfation patterns for FGF activation and provided new insights into the saccharide structures involved. Altogether, our data bring to light an original processive enzymatic mechanism, by which HSulfs catalyze oriented alteration of HS 6-O-desulfation patterns and direct fine and differential regulation of HS functions.
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Affiliation(s)
- Amal Seffouh
- Institut de Biologie Structurale Jean-Pierre Ebel, Unité Mixte de Recherche 5075, Centre National de la Recherche Scientifique-Commissariat à l'Énergie Atomique et aux Énergies Alternatives-Université Joseph Fourier, Grenoble, France
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12
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Hou Y, Genua M, Tada Batista D, Calemczuk R, Buhot A, Fornarelli P, Koubachi J, Bonnaffé D, Saesen E, Laguri C, Lortat-Jacob H, Livache T. Continuous evolution profiles for electronic-tongue-based analysis. Angew Chem Int Ed Engl 2012; 51:10394-8. [PMID: 22968809 DOI: 10.1002/anie.201205346] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Yanxia Hou
- SPrAM, UMR 5819 (CEA-CNRS-UJF-Grenoble 1), INAC/CEA-Grenoble, 38054 Grenoble cedex 9, France.
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13
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Hou Y, Genua M, Tada Batista D, Calemczuk R, Buhot A, Fornarelli P, Koubachi J, Bonnaffé D, Saesen E, Laguri C, Lortat-Jacob H, Livache T. Continuous Evolution Profiles for Electronic-Tongue-Based Analysis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Laguri C, Sapay N, Simorre JP, Brutscher B, Imberty A, Gans P, Lortat-Jacob H. 13C-labeled heparan sulfate analogue as a tool to study protein/heparan sulfate interactions by NMR spectroscopy: application to the CXCL12α chemokine. J Am Chem Soc 2011; 133:9642-5. [PMID: 21634378 DOI: 10.1021/ja201753e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heparan sulfate (HS), a polysaccharide of the glycosaminoglycan family characterized by a unique level of complexity, has emerged as a key regulator of many fundamental biological processes. Although it has become clear that this class of molecules exert their functions by interacting with proteins, the exact modes of interaction still remain largely unknown. Here we report the engineering of a (13)C-labeled HS-like oligosaccharide with a defined oligosaccharidic sequence that was used to investigate the structural determinants involved in protein/HS recognition by multidimensional NMR spectroscopy. Using the chemokine CXCL12α as a model system, we obtained experimental NMR data on both the oligosaccharide and the chemokine that was used to obtain a structural model of a protein/HS complex. This new approach provides a foundation for further investigations of protein/HS interactions and should find wide application.
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Affiliation(s)
- Cédric Laguri
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, F-38027 Grenoble Cedex 1, France.
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15
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Jasnin M, van Eijck L, Marek Koza M, Peters J, Laguri C, Lortat-Jacob H, Zaccai G. Dynamics of heparan sulfate explored by neutron scattering. Phys Chem Chem Phys 2010; 12:3360-2. [DOI: 10.1039/b923878f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Laguri C, Duband-Goulet I, Friedrich N, Axt M, Belin P, Callebaut I, Gilquin B, Zinn-Justin S, Couprie J. Human mismatch repair protein MSH6 contains a PWWP domain that targets double stranded DNA. Biochemistry 2008; 47:6199-207. [PMID: 18484749 DOI: 10.1021/bi7024639] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic mismatch repair (MMR) protein MSH6 exhibits a core region structurally and functionally similar to bacterial MutS. However, it possesses an additional N-terminal region (NTR), comprising a PCNA binding motif, a large region of unknown function and a nonspecific DNA binding fragment. Yeast NTR was recently described as an extended tether between PCNA and the core of MSH6 . In contrast, we show that human NTR presents a globular PWWP domain in the region of unknown function. We demonstrate that this PWWP domain binds double-stranded DNA, without any preference for mismatches or nicks, whereas its apparent affinity for single-stranded DNA is about 20 times lower. The S144I mutation, which in human MSH6 causes inherited somatic defects in MMR resulting in increased development of hereditary non polyposis colorectal cancer , is located in the DNA binding surface of the PWWP domain. However, it only moderately affects domain stability, and it does not perturb DNA binding in vitro.
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Affiliation(s)
- Cédric Laguri
- CEA Laboratoire de Biologie Structurale et Radiobiologie, iBiTec-Saclay, 91191 Gif sur Yvette, France
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Laguri C, Arenzana-Seisdedos F, Lortat-Jacob H. Relationships between glycosaminoglycan and receptor binding sites in chemokines-the CXCL12 example. Carbohydr Res 2008; 343:2018-23. [PMID: 18334249 DOI: 10.1016/j.carres.2008.01.047] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 01/24/2008] [Accepted: 01/29/2008] [Indexed: 11/30/2022]
Abstract
Chemokines are small proteins, promoting directional migration and activation of different cells through binding to specific receptors. Most chemokines also bind to heparan sulfate (HS), a family of complex and highly sulfated glycosaminoglycan (GAG) found at the cell surface and in the extracellular matrix. This class of molecules has recently emerged as critical regulators of many events involving cell response to the external environment. Binding to HS is thought to be functionally important. Current models suggested that HS ensures the correct positioning of chemokines within tissues and maintains haptotactic gradients of the proteins along cell surfaces, thus providing directional cues for migrating cells. On the chemokine surface, the GAG binding epitopes can be displayed on different areas, some of which overlap the receptor binding domain, while others are clearly separated. We review here some structural aspects of the interaction between GAGs or receptors and chemokines. In particular, we will address the case of CXCL12, a chemokine whose receptor binding site is distinct from the GAG binding site and whose different isoforms display different GAG binding abilities. This chemokine system thus offers an unprecedented opportunity to ascertain the importance of chemokine/GAG interaction in the regulation of cell migration.
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Affiliation(s)
- Cédric Laguri
- IBS, Institut de Biologie Structurale, UMR 5075 CNRS CEA UJF 41 rue Horowitz, F-38027 Grenoble, France
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Laguri C, Stenzel RA, Donohue TJ, Phillips-Jones MK, Williamson MP. Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides. Biochemistry 2006; 45:7872-81. [PMID: 16784239 PMCID: PMC2517121 DOI: 10.1021/bi060683g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PrrA is a global transcription regulator activated upon phosphorylation by its cognate kinase PrrB in response to low oxygen levels in Rhodobacter sphaeroides. Here we show by gel filtration, analytical ultracentrifugation, and NMR diffusion measurements that treatment of PrrA with a phosphate analogue, BeF(3)(-), results in dimerization of the protein, producing a protein that binds DNA. No dimeric species was observed in the absence of BeF(3)(-). Upon addition of BeF(3)(-), the inhibitory activity of the N-terminal domain on the C-terminal DNA-binding domain is relieved, after which PrrA becomes capable of binding DNA as a dimer. The interaction surface of the DNA-binding domain with the regulatory domain of PrrA is identified by NMR as being a well-conserved region centered on helix alpha6, which is on the face opposite from the DNA recognition helix. This suggests that there is no direct blockage of DNA binding in the inactive state but rather that PrrA dimerization promotes a correct arrangement of two adjacent DNA-binding domains that recognizes specific DNA binding sequences.
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Affiliation(s)
- Cédric Laguri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, UK
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Laguri C, Phillips-Jones MK, Williamson MP. Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity. Nucleic Acids Res 2004; 31:6778-87. [PMID: 14627811 PMCID: PMC290259 DOI: 10.1093/nar/gkg891] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Prr/RegA response regulator is a global transcription regulator in purple bacteria Rhodobacter sphaeroides and Rhodobacter capsulatus, and is essential in controlling the metabolic changes between aerobic and anaerobic environments. We report here the structure determination by NMR of the C-terminal effector domain of PrrA, PrrAC. It forms a three-helix bundle containing a helix-turn-helix DNA binding motif. The fold is similar to FIS protein, but the domain architecture is different from previously characterised response regulator effector domains, as it is shorter than any characterised so far. Alignment of Prr/RegA DNA targets permitted a refinement of the consensus sequence, which contains two GCGNC inverted repeats with variable half-site spacings. NMR titrations of PrrAC with specific and non-specific DNA show which surfaces are involved in DNA binding and suggest residues important for binding specificity. A model of the PrrAC/DNA complex was constructed in which two PrrAC molecules are bound to DNA in a symmetrical manner.
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Affiliation(s)
- Cédric Laguri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2UH, UK
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Laguri C, Gilquin B, Wolff N, Romi-Lebrun R, Courchay K, Callebaut I, Worman HJ, Zinn-Justin S. Structural characterization of the LEM motif common to three human inner nuclear membrane proteins. Structure 2001; 9:503-11. [PMID: 11435115 DOI: 10.1016/s0969-2126(01)00611-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Integral membrane proteins of the inner nuclear membrane are involved in chromatin organization and postmitotic reassembly of the nucleus. The discovery that mutations in the gene encoding emerin causes X-linked Emery-Dreifuss muscular dystrophy has enhanced interest in such proteins. A common structural domain of 50 residues, called the LEM domain, has been identified in emerin MAN1, and lamina-associated polypeptide (LAP) 2. In particular, all LAP2 isoforms share an N-terminal segment composed of such a LEM domain that is connected to a highly divergent LEM-like domain by a linker that is probably unstructured. RESULTS We have determined the three-dimensional structures of the LEM and LEM-like domains of LAP2 using nuclear magnetic resonance and molecular modeling. Both domains adopt the same fold, mainly composed of two large parallel alpha helices. CONCLUSIONS The structural LEM motif is found in human inner nuclear membrane proteins and in protein-protein interaction domains from bacterial multienzyme complexes. This suggests that LEM and LEM-like domains are protein-protein interaction domains. A region conserved in all LEM domains, at the surface of helix 2, could mediate interaction between LEM domains and a common protein partner.
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Affiliation(s)
- C Laguri
- Département d'Ingénierie et d'Etudes des Protéines, CEA Saclay, 91191, Gif-sur-Yvette, France
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