1
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van der Gracht D, Rowland RJ, Roig-Zamboni V, Ferraz MJ, Louwerse M, Geurink PP, Aerts JMFG, Sulzenbacher G, Davies GJ, Overkleeft HS, Artola M. Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Chem Sci 2023; 14:9136-9144. [PMID: 37655021 PMCID: PMC10466331 DOI: 10.1039/d3sc01021j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
Lysosomal exoglycosidases are responsible for processing endocytosed glycans from the non-reducing end to produce the corresponding monosaccharides. Genetic mutations in a particular lysosomal glycosidase may result in accumulation of its particular substrate, which may cause diverse lysosomal storage disorders. The identification of effective therapeutic modalities to treat these diseases is a major yet poorly realised objective in biomedicine. One common strategy comprises the identification of effective and selective competitive inhibitors that may serve to stabilize the proper folding of the mutated enzyme, either during maturation and trafficking to, or residence in, endo-lysosomal compartments. The discovery of such inhibitors is greatly aided by effective screening assays, the development of which is the focus of the here-presented work. We developed and applied fluorescent activity-based probes reporting on either human GH30 lysosomal glucosylceramidase (GBA1, a retaining β-glucosidase) or GH31 lysosomal retaining α-glucosidase (GAA). FluoPol-ABPP screening of our in-house 358-member iminosugar library yielded compound classes selective for either of these enzymes. In particular, we identified a class of N-alkyldeoxynojirimycins that inhibit GAA, but not GBA1, and that may form the starting point for the development of pharmacological chaperone therapeutics for the lysosomal glycogen storage disease that results from genetic deficiency in GAA: Pompe disease.
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Affiliation(s)
- Daniël van der Gracht
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Rhianna J Rowland
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Véronique Roig-Zamboni
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Maria J Ferraz
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Max Louwerse
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2333 ZC Leiden The Netherlands
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Gerlind Sulzenbacher
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
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2
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Barelier S, Avellan R, Gnawali GR, Fourquet P, Roig-Zamboni V, Poncin I, Point V, Bourne Y, Audebert S, Camoin L, Spilling CD, Canaan S, Cavalier JF, Sulzenbacher G. Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis. FEBS J 2023; 290:1563-1582. [PMID: 36197115 DOI: 10.1111/febs.16645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 08/25/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
Abstract
A hallmark of Mycobacterium tuberculosis (M. tb), the aetiologic agent of tuberculosis, is its ability to metabolise host-derived lipids. However, the enzymes and mechanisms underlying such metabolism are still largely unknown. We previously reported that the Cyclophostin & Cyclipostins (CyC) analogues, a new family of potent antimycobacterial molecules, react specifically and covalently with (Ser/Cys)-based enzymes mostly involved in bacterial lipid metabolism. Here, we report the synthesis of new CyC alkyne-containing inhibitors (CyCyne ) and their use for the direct fishing of target proteins in M. tb culture via bio-orthogonal click-chemistry activity-based protein profiling (CC-ABPP). This approach led to the capture and identification of a variety of enzymes, and many of them involved in lipid or steroid metabolisms. One of the captured enzymes, HsaD (Rv3569c), is required for the survival of M. tb within macrophages and is thus a potential therapeutic target. This prompted us to further explore and validate, through a combination of biochemical and structural approaches, the specificity of HsaD inhibition by the CyC analogues. We confirmed that the CyC bind covalently to the catalytic Ser114 residue, leading to a total loss of enzyme activity. These data were supported by the X-ray structures of four HsaD-CyC complexes, obtained at resolutions between 1.6 and 2.6 Å. The identification of mycobacterial enzymes directly captured by the CyCyne probes through CC-ABPP paves the way to better understand and potentially target key players at crucial stages of the bacilli life cycle.
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Affiliation(s)
| | - Romain Avellan
- CNRS, LISM, IMM FR3479, Aix-Marseille University, France
| | - Giri Raj Gnawali
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, MO, USA
| | - Patrick Fourquet
- INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Aix-Marseille University, France
| | | | | | - Vanessa Point
- CNRS, LISM, IMM FR3479, Aix-Marseille University, France
| | - Yves Bourne
- CNRS, AFMB, Aix-Marseille University, France
| | - Stéphane Audebert
- INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Aix-Marseille University, France
| | - Luc Camoin
- INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Aix-Marseille University, France
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3
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Kok K, Kuo CL, Katzy RE, Lelieveld LT, Wu L, Roig-Zamboni V, van der Marel GA, Codée JDC, Sulzenbacher G, Davies GJ, Overkleeft HS, Aerts JMFG, Artola M. 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal α-Glucosidase Stabilizer for the Treatment of Pompe Disease. J Am Chem Soc 2022; 144:14819-14827. [PMID: 35917590 PMCID: PMC9389588 DOI: 10.1021/jacs.2c05666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
α-Glucosidase inhibitors are potential therapeutics
for the
treatment of diabetes, viral infections, and Pompe disease. Herein,
we report a 1,6-epi-cyclophellitol cyclosulfamidate
as a new class of reversible α-glucosidase inhibitors that displays
enzyme inhibitory activity by virtue of its conformational mimicry
of the substrate when bound in the Michaelis complex. The α-d-glc-configured cyclophellitol cyclosulfamidate 4 binds in a competitive manner the human lysosomal acid α-glucosidase
(GAA), ER α-glucosidases, and, at higher concentrations, intestinal
α-glucosidases, displaying an excellent selectivity over the
human β-glucosidases GBA and GBA2 and glucosylceramide synthase
(GCS). Cyclosulfamidate 4 stabilizes recombinant human
GAA (rhGAA, alglucosidase alfa, Myozyme) in cell medium and plasma
and facilitates enzyme trafficking to lysosomes. It stabilizes rhGAA
more effectively than existing small-molecule chaperones and does
so in vitro, in cellulo, and in vivo in zebrafish, thus representing a promising therapeutic
alternative to Miglustat for Pompe disease.
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Affiliation(s)
- Ken Kok
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Chi-Lin Kuo
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Rebecca E Katzy
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Lindsey T Lelieveld
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Liang Wu
- Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Véronique Roig-Zamboni
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille 13288, France
| | - Gijsbert A van der Marel
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Jeroen D C Codée
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gerlind Sulzenbacher
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille 13288, France
| | - Gideon J Davies
- Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Herman S Overkleeft
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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4
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Roig-Zamboni V, Barelier S, Dixon R, Galley NF, Ghanem A, Nguyen QP, Cahuzac H, Salamaga B, Davis PJ, Bourne Y, Mesnage S, Vincent F. Molecular basis for substrate recognition and septum cleavage by AtlA, the major N-acetylglucosaminidase of Enterococcus faecalis. J Biol Chem 2022; 298:101915. [PMID: 35398351 PMCID: PMC9108991 DOI: 10.1016/j.jbc.2022.101915] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022] Open
Abstract
The cleavage of septal peptidoglycan at the end of cell division facilitates the separation of the two daughter cells. The hydrolases involved in this process (called autolysins) are potentially lethal enzymes that can cause cell death; their activity, therefore, must be tightly controlled during cell growth. In Enterococcus faecalis, the N-acetylglucosaminidase AtlA plays a predominant role in cell separation. atlA mutants form long cell chains and are significantly less virulent in the zebrafish model of infection. The attenuated virulence of atlA mutants is underpinned by a limited dissemination of bacterial chains in the host organism and a more efficient uptake by phagocytes that clear the infection. AtlA has structural homologs in other important pathogens, such as Listeria monocytogenes and Salmonella typhimurium, and therefore represents an attractive model to design new inhibitors of bacterial pathogenesis. Here, we provide a 1.45 Å crystal structure of the E. faecalis AtlA catalytic domain that reveals a closed conformation of a conserved β-hairpin and a complex network of hydrogen bonds that bring two catalytic residues to the ideal distance for an inverting mechanism. Based on the model of the AtlA-substrate complex, we identify key residues critical for substrate recognition and septum cleavage during bacterial growth. We propose that this work will provide useful information for the rational design of specific inhibitors targeting this enterococcal virulence factor and its orthologs in other pathogens.
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Affiliation(s)
| | | | - Robert Dixon
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Nicola F Galley
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Amani Ghanem
- CNRS, Aix Marseille University, AFMB, Marseille, France
| | | | - Héloize Cahuzac
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Peter J Davis
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Yves Bourne
- CNRS, Aix Marseille University, AFMB, Marseille, France
| | - Stéphane Mesnage
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom.
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5
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Iacono R, Minopoli N, Ferrara MC, Tarallo A, Damiano C, Porto C, Strollo S, Roig-Zamboni V, Peluso G, Sulzenbacher G, Cobucci-Ponzano B, Parenti G, Moracci M. Carnitine is a pharmacological allosteric chaperone of the human lysosomal α-glucosidase. J Enzyme Inhib Med Chem 2021; 36:2068-2079. [PMID: 34565280 PMCID: PMC8477953 DOI: 10.1080/14756366.2021.1975694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 11/22/2022] Open
Abstract
Pompe disease is an inherited metabolic disorder due to the deficiency of the lysosomal acid α-glucosidase (GAA). The only approved treatment is enzyme replacement therapy with the recombinant enzyme (rhGAA). Further approaches like pharmacological chaperone therapy, based on the stabilising effect induced by small molecules on the target enzyme, could be a promising strategy. However, most known chaperones could be limited by their potential inhibitory effects on patient’s enzymes. Here we report on the discovery of novel chaperones for rhGAA, L- and D-carnitine, and the related compound acetyl-D-carnitine. These drugs stabilise the enzyme at pH and temperature without inhibiting the activity and acted synergistically with active-site directed pharmacological chaperones. Remarkably, they enhanced by 4-fold the acid α-glucosidase activity in fibroblasts from three Pompe patients with added rhGAA. This synergistic effect of L-carnitine and rhGAA has the potential to be translated into improved therapeutic efficacy of ERT in Pompe disease.
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Affiliation(s)
- Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and Bioresources - CNR, Naples, Italy
| | - Nadia Minopoli
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | | | | | - Carla Damiano
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Caterina Porto
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Sandra Strollo
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Véronique Roig-Zamboni
- Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, AFMB, Marseille, France
| | - Gianfranco Peluso
- Research Institute on Terrestrial Ecosystems, UOS Naples-CNR, Naples, Italy
| | - Gerlind Sulzenbacher
- Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, AFMB, Marseille, France
| | | | - Giancarlo Parenti
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy.,Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and Bioresources - CNR, Naples, Italy
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6
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Valle C, Martin B, Ferron F, Roig-Zamboni V, Desmyter A, Debart F, Vasseur JJ, Canard B, Coutard B, Decroly E. First insights into the structural features of Ebola virus methyltransferase activities. Nucleic Acids Res 2021; 49:1737-1748. [PMID: 33503246 PMCID: PMC7897494 DOI: 10.1093/nar/gkaa1276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
The Ebola virus is a deadly human pathogen responsible for several outbreaks in Africa. Its genome encodes the 'large' L protein, an essential enzyme that has polymerase, capping and methyltransferase activities. The methyltransferase activity leads to RNA co-transcriptional modifications at the N7 position of the cap structure and at the 2'-O position of the first transcribed nucleotide. Unlike other Mononegavirales viruses, the Ebola virus methyltransferase also catalyses 2'-O-methylation of adenosines located within the RNA sequences. Herein, we report the crystal structure at 1.8 Å resolution of the Ebola virus methyltransferase domain bound to a fragment of a camelid single-chain antibody. We identified structural determinants and key amino acids specifically involved in the internal adenosine-2'-O-methylation from cap-related methylations. These results provide the first high resolution structure of an ebolavirus L protein domain, and the framework to investigate the effects of epitranscriptomic modifications and to design possible antiviral drugs against the Filoviridae family.
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Affiliation(s)
- Coralie Valle
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Baptiste Martin
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - François Ferron
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Véronique Roig-Zamboni
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Aline Desmyter
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Françoise Debart
- IBMM, UMR 5247 CNRS, Université de Montpellier, ENSCM, Montpellier, France
| | | | - Bruno Canard
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm, 1207-IHU Méditerranée Infection) Marseille, France
| | - Etienne Decroly
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
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7
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Nguyen NT, Vivès RR, Torres M, Delauzun V, Saesen E, Roig-Zamboni V, Lortat-Jacob H, Rihet P, Bourne Y. Genetic and enzymatic characterization of 3-O-sulfotransferase SNPs associated with Plasmodium falciparum parasitaemia. Glycobiology 2018; 28:534-541. [PMID: 29718295 DOI: 10.1093/glycob/cwy038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/27/2018] [Indexed: 01/09/2023] Open
Abstract
The HS3ST3A1/B1 genes encode two homologous 3-O-sulfotransferases involved in the late modification step during heparan sulfate (HS) biosynthesis. In addition to the single nucleotide polymorphisms (SNPs) rs28470223 (C > T) in the promoter region of both HS3ST3A1 and rs62636623 (Gly/Arg) in the stem region of HS3ST3B1, three missense mutations (rs62056073, rs61729712 and rs9906590) located within the catalytic sulfotransferase domain of 3-OST-B1 are linked and associated to Plasmodium falciparum parasitaemia. To ascertain the functional effects of these SNP associations, we investigated the regulatory effect of rs28470223 and characterized the enzymatic activity of the missense SNP rs61729712 (Ser279Asn) localized at proximity of the substrate binding cleft. The SNP rs28470223 results in decreased promoter activity of HS3ST3A1 in K562 cells, suggesting a reduced in vivo transcription activity of the target gene. A comparative kinetic analysis of wt HS3ST3B1 and the Ser269Asn variant (rs61729712) using a HS-derived oligosaccharide substrate reveals a slightly higher catalytic activity for the SNP variant. These genetic and enzymatic studies suggest that genetic variations in enzymes responsible of HS 3-O-sulfation can modulate their promoter and enzymatic activities and may influence P. falciparum parasitaemia.
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Affiliation(s)
- Ngoc Thy Nguyen
- Aix Marseille University, INSERM, TAGC, Marseille, France.,CNRS, Aix Marseille University, AFMB, Marseille, France
| | - Romain R Vivès
- University of Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Magali Torres
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | | | - Els Saesen
- University of Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Pascal Rihet
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | - Yves Bourne
- CNRS, Aix Marseille University, AFMB, Marseille, France
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8
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Sulzenbacher G, Roig-Zamboni V, Lebrun R, Guérardel Y, Murat D, Mansuelle P, Yamakawa N, Qian XX, Vincentelli R, Bourne Y, Wu LF, Alberto F. Glycosylate and move! The glycosyltransferase Maf is involved in bacterial flagella formation. Environ Microbiol 2017; 20:228-240. [DOI: 10.1111/1462-2920.13975] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/17/2017] [Accepted: 10/22/2017] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Régine Lebrun
- Plate-forme Protéomique; Institut de Microbiologie de la Méditerranée, FR3479 Aix-Marseille Université and Centre National de la Recherche Scientifique; Marseille 13402 France
| | - Yann Guérardel
- Unité de Glycobiologie Structurale et Fonctionnelle; UMR 8576 Université de Lille and Centre National de la Recherche Scientifique; Lille 59000 France
| | - Dorothée Murat
- Aix Marseille Univ, CNRS, LCB UMR7283; Marseille 13402 France
- International Associated Laboratory of Evolution and Development of Magnetotactic Organisms (LIA-MagMC); Centre National de la Recherche Scientifique; Marseille 13402 France
| | - Pascal Mansuelle
- Plate-forme Protéomique; Institut de Microbiologie de la Méditerranée, FR3479 Aix-Marseille Université and Centre National de la Recherche Scientifique; Marseille 13402 France
| | - Nao Yamakawa
- Unité de Glycobiologie Structurale et Fonctionnelle; UMR 8576 Université de Lille and Centre National de la Recherche Scientifique; Lille 59000 France
| | - Xin-Xin Qian
- Aix Marseille Univ, CNRS, LCB UMR7283; Marseille 13402 France
- International Associated Laboratory of Evolution and Development of Magnetotactic Organisms (LIA-MagMC); Centre National de la Recherche Scientifique; Marseille 13402 France
| | | | - Yves Bourne
- Aix Marseille Univ, CNRS, AFMB UMR7257; Marseille 13288 France
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB UMR7283; Marseille 13402 France
- International Associated Laboratory of Evolution and Development of Magnetotactic Organisms (LIA-MagMC); Centre National de la Recherche Scientifique; Marseille 13402 France
| | - François Alberto
- Aix Marseille Univ, CNRS, LCB UMR7283; Marseille 13402 France
- International Associated Laboratory of Evolution and Development of Magnetotactic Organisms (LIA-MagMC); Centre National de la Recherche Scientifique; Marseille 13402 France
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9
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Sulzenbacher G, Roig-Zamboni V, Peumans WJ, Henrissat B, van Damme EJM, Bourne Y. Structural basis for carbohydrate binding properties of a plant chitinase-like agglutinin with conserved catalytic machinery. J Struct Biol 2015; 190:115-21. [PMID: 25727185 DOI: 10.1016/j.jsb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 01/13/2023]
Abstract
A new chitinase-like agglutinin, RobpsCRA, related to family GH18 chitinases, has previously been identified in black locust (Robinia pseudoacacia) bark. The crystal structure of RobpsCRA at 1.85Å resolution reveals unusual molecular determinants responsible for the lack of its ancestral chitinase activity. Unlike other chitinase-like proteins, which lack chitinase catalytic residues, RobpsCRA has conserved its catalytic machinery. However, concerted rearrangements of loop regions coupled to non-conservative substitutions of aromatic residues central to the chitin-binding groove explain the lack of hydrolytic activity against chitin and the switch toward recognition of high-mannose type N-glycans. Identification of close homologs in flowering plants with conservation of sequence motifs associated to the structural adaptations seen in RobpsCRA defines an emerging class of agglutinins, as emphasized by a phylogenetic analysis, that are likely to share a similar carbohydrate binding specificity for high-mannose type N-glycans. This study illustrates the recent evolution and molecular adaptation of a versatile TIM-barrel scaffold within the ancestral GH18 family.
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Affiliation(s)
- Gerlind Sulzenbacher
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Véronique Roig-Zamboni
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Willy J Peumans
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Bernard Henrissat
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Els J M van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Yves Bourne
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
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10
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Sulzenbacher G, Roig-Zamboni V, Peumans WJ, Rougé P, Van Damme EJ, Bourne Y. Crystal structure of the GalNAc/Gal-specific agglutinin from the phytopathogenic ascomycete Sclerotinia sclerotiorum reveals novel adaptation of a beta-trefoil domain. J Mol Biol 2010; 400:715-23. [PMID: 20566411 PMCID: PMC2956877 DOI: 10.1016/j.jmb.2010.05.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
A lectin from the phytopathogenic ascomycete Sclerotinia sclerotiorum that shares only weak sequence similarity with characterized fungal lectins has recently been identified. S. sclerotiorum agglutinin (SSA) is a homodimeric protein consisting of two identical subunits of approximately 17 kDa and displays specificity primarily towards Gal/GalNAc. Glycan array screening indicates that SSA readily interacts with Gal/GalNAc-bearing glycan chains. The crystal structures of SSA in the ligand-free form and in complex with the Gal-beta1,3-GalNAc (T-antigen) disaccharide have been determined at 1.6 and 1.97 A resolution, respectively. SSA adopts a beta-trefoil domain as previously identified for other carbohydrate-binding proteins of the ricin B-like lectin superfamily and accommodates terminal non-reducing galactosyl and N-acetylgalactosaminyl glycans. Unlike other structurally related lectins, SSA contains a single carbohydrate-binding site at site alpha. SSA reveals a novel dimeric assembly markedly dissimilar to those described earlier for ricin-type lectins. The present structure exemplifies the adaptability of the beta-trefoil domain in the evolution of fungal lectins.
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Affiliation(s)
- Gerlind Sulzenbacher
- Architecture et Fonction des Macromolécules Biologiques (AFMB, UMR-6098) CNRS, Université Aix-Marseille, Campus Luminy, Case 932, F-13288 Marseille cedex 09, France
| | - Véronique Roig-Zamboni
- Architecture et Fonction des Macromolécules Biologiques (AFMB, UMR-6098) CNRS, Université Aix-Marseille, Campus Luminy, Case 932, F-13288 Marseille cedex 09, France
| | - Willy J. Peumans
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, Ghent, Belgium
| | - Pierre Rougé
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR-CNRS 5546, Pôle de Biotechnologie Végétale, Toulouse, France
| | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, Ghent, Belgium
| | - Yves Bourne
- Architecture et Fonction des Macromolécules Biologiques (AFMB, UMR-6098) CNRS, Université Aix-Marseille, Campus Luminy, Case 932, F-13288 Marseille cedex 09, France
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11
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Sulzenbacher G, Canaan S, Bordat Y, Neyrolles O, Stadthagen G, Roig-Zamboni V, Rauzier J, Maurin D, Laval F, Daffé M, Cambillau C, Gicquel B, Bourne Y, Jackson M. LppX is a lipoprotein required for the translocation of phthiocerol dimycocerosates to the surface of Mycobacterium tuberculosis. EMBO J 2006; 25:1436-44. [PMID: 16541102 PMCID: PMC1440309 DOI: 10.1038/sj.emboj.7601048] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Accepted: 02/20/2006] [Indexed: 11/09/2022] Open
Abstract
Cell envelope lipids play an important role in the pathogenicity of mycobacteria, but the mechanisms by which they are transported to the outer membrane of these prokaryotes are largely unknown. Here, we provide evidence that LppX is a lipoprotein required for the translocation of complex lipids, the phthiocerol dimycocerosates (DIM), to the outer membrane of Mycobacterium tuberculosis. Abolition of DIM transport following disruption of the lppX gene is accompanied by an important attenuation of the virulence of the tubercle bacillus. The crystal structure of LppX unveils an U-shaped beta-half-barrel dominated by a large hydrophobic cavity suitable to accommodate a single DIM molecule. LppX shares a similar fold with the periplasmic molecular chaperone LolA and the outer membrane lipoprotein LolB, which are involved in the localization of lipoproteins to the outer membrane of Gram-negative bacteria. Based on the structure and although an indirect participation of LppX in DIM transport cannot yet be ruled out, we propose LppX to be the first characterized member of a family of structurally related lipoproteins that carry lipophilic molecules across the mycobacterial cell envelope.
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Affiliation(s)
| | - Stéphane Canaan
- AFMB, CNRS UMR 6098, Marseille Cedex, France
- Laboratoire d'Enzymologie Interfaciale et de Physiologie de la Lipolyse CNRS UPR 9025, Marseille Cedex, France
| | - Yann Bordat
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
| | - Olivier Neyrolles
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
| | - Gustavo Stadthagen
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
| | | | - Jean Rauzier
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
| | | | - Françoise Laval
- Département ‘Mécanismes Moléculaires des Infections Mycobactériennes', Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Université Paul Sabatier, Toulouse Cedex, France
| | - Mamadou Daffé
- Département ‘Mécanismes Moléculaires des Infections Mycobactériennes', Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Université Paul Sabatier, Toulouse Cedex, France
| | | | - Brigitte Gicquel
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
| | - Yves Bourne
- AFMB, CNRS UMR 6098, Marseille Cedex, France
- AFMB, CNRS UMR 6098, Case 932 Campus de Luminy, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France. Tel.: +33 4 91 82 55 66; Fax: +33 4 91 26 67 20; E-mail:
| | - Mary Jackson
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris Cedex, France
- Unité de Génétique Mycobactérienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France. Tel.: +33 1 45 68 88 77; Fax: +33 1 45 68 88 43; E-mail:
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12
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Canaan S, Sulzenbacher G, Roig-Zamboni V, Scappuccini-Calvo L, Frassinetti F, Maurin D, Cambillau C, Bourne Y. Crystal structure of the conserved hypothetical protein Rv1155 from Mycobacterium tuberculosis. FEBS Lett 2005; 579:215-21. [PMID: 15620716 DOI: 10.1016/j.febslet.2004.11.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 11/16/2004] [Accepted: 11/21/2004] [Indexed: 11/27/2022]
Abstract
With the aim of elucidating the biological function of hypothetical proteins unique amongst the Actynomyces sub-group of bacteria, we have solved the crystal structure of the conserved hypothetical protein Rv1155 from Mycobacterium tuberculosis at 1.8 A resolution. Rv1155 is a homodimer both in the crystal structure and in solution and folds into two separate domains consisting of a six-stranded anti-parallel beta-barrel fold flanked by two alpha-helices and a helix-turn-helix domain. Both domains contribute to the formation of two deep clefts at the dimer interface. The overall fold of Rv1155 strikingly resembles that of flavin mononucleotide-binding protein and pyridoxamine 5'-phosphate oxydase, but the architecture of the putative binding pocket is markedly different, consistent with the lack of color of Rv1155 and its inability to bind FMN. Rv1155 thus appears to belong to a group of proteins with stringent conservation of the binding cleft, having evolved towards a new binding function.
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Affiliation(s)
- Stéphane Canaan
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France
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13
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Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J Mol Biol 2004; 343:29-41. [PMID: 15381418 DOI: 10.1016/j.jmb.2004.08.030] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Revised: 07/30/2004] [Accepted: 08/10/2004] [Indexed: 11/17/2022]
Abstract
In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2.1.8), catalysing the oxidation of betaine aldehyde into glycine betaine. The structure of YdcW resembles that of other aldehyde dehydrogenases: it is tetrameric and binds a NADH molecule in each monomer. The NADH molecules, bound in the active site by soaking, are revealed to be in the "hydrolysis position". Activities experiments demonstrate that YdcW is more active on medium-chains aldehyde than on betaine aldehyde. However, soaking of betaine into YdcW crystals revealed its presence in one of the subunits, in two positions, a putative resting position and a hydride transfer ready position. Analysis of kinetics data and of the active site shape suggest an optimum binding of n-alkyl aldehydes up to seven to eight carbon atoms, possibly followed by a bulky cyclic or aromatic group.
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Affiliation(s)
- Arnaud Gruez
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France
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14
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Sulzenbacher G, Roig-Zamboni V, Pagot F, Grisel S, Salomoni A, Valencia C, Campanacci V, Vincentelli R, Tegoni M, Eklund H, Cambillau C. Structure ofEscherichia coliYhdH, a putative quinone oxidoreductase. Acta Crystallogr D Biol Crystallogr 2004; 60:1855-62. [PMID: 15388933 DOI: 10.1107/s0907444904020220] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 08/16/2004] [Indexed: 11/10/2022]
Abstract
As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The overall fold of YhdH is very similar to that of alcohol dehydrogenases and quinone reductases despite its low sequence identity. The absence of any Zn ion indicates that YdhH is a putative quinone oxidoreductase. YhdH forms a homodimer, with each subunit composed of two domains: a catalytic domain and a coenzyme-binding domain. NADP is bound in a deep cleft formed between the two domains. Large conformational changes occur upon NADP binding, with the two domains closing up to each other and narrowing the NADP-binding cleft. Comparisons of the YdhH active site with those of the quinone oxidoreductases from Escherichia coli and Thermus thermophilus made it possible to identify essential conserved residues as being Asn41, Asp43, Asp64 and Arg318. The active-site size is very narrow and unless an induced fit occurs is accessible only to reagents the size of benzoquinone.
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Affiliation(s)
- Gerlind Sulzenbacher
- AFMB, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 Chemin J. Aiguier, F-13402 Marseille 20, France
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15
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Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett 2004; 571:141-6. [PMID: 15280032 DOI: 10.1016/j.febslet.2004.06.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 06/16/2004] [Accepted: 06/28/2004] [Indexed: 11/21/2022]
Abstract
The ybdL gene of Escherichia coli codes for a protein of unknown function. Sequence analysis showed moderate homology to several vitamin B(6) dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The structure analysis of YbdL to 2.35 A resolution by protein crystallography verifies that it is a PLP dependent enzyme of fold type I, the typical aspartate aminotransferase fold. The active site contains a bound pyridoxal-5'-phosphate, covalently attached to the conserved active site lysine residue Lys236. The pattern of conserved amino acids in the putative substrate binding pocket of the enzyme reveals that it is most closely related to a hyperthermophilic aromatic residue aminotransferase from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids as amino-donors reveal, however, a preference for Met, followed by His and Phe, results which can be rationalized by modelization studies.
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Affiliation(s)
- Manuela Dolzan
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités d'Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France
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16
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Grassick A, Sulzenbacher G, Roig-Zamboni V, Campanacci V, Cambillau C, Bourne Y. Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase. Proteins 2004; 55:764-7. [PMID: 15103639 DOI: 10.1002/prot.20025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alice Grassick
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR6098, Marseille, France
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17
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Bourne Y, Roig-Zamboni V, Barre A, Peumans WJ, Astoul CH, Van Damme EJM, Rougé P. The crystal structure of the Calystegia sepium agglutinin reveals a novel quaternary arrangement of lectin subunits with a beta-prism fold. J Biol Chem 2003; 279:527-33. [PMID: 14561768 DOI: 10.1074/jbc.m308218200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [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: 12/11/2022] Open
Abstract
The high number of quaternary structures observed for lectins highlights the important role of these oligomeric assemblies during carbohydrate recognition events. Although a large diversity in the mode of association of lectin subunits is frequently observed, the oligomeric assemblies of plant lectins display small variations within a single family. The crystal structure of the mannose-binding jacalin-related lectin from Calystegia sepium (Calsepa) has been determined at 1.37-A resolution. Calsepa exhibits the same beta-prism fold as identified previously for other members of the family, but the shape and the hydrophobic character of its carbohydrate-binding site is unlike that of other members, consistent with surface plasmon resonance analysis showing a preference for methylated sugars. Calsepa reveals a novel dimeric assembly markedly dissimilar to those described earlier for Heltuba and jacalin but mimics the canonical 12-stranded beta-sandwich dimer found in legume lectins. The present structure exemplifies the adaptability of the beta-prism building block in the evolution of plant lectins and highlights the biological role of these quaternary structures for carbohydrate recognition.
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Affiliation(s)
- Yves Bourne
- AFMB-CNRS, CNRS UMR6098, F13402 Marseille Cedex 20, France.
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18
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Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C. The crystal structure of the Escherichia coli YfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases. J Biol Chem 2003; 278:34582-6. [PMID: 12844490 DOI: 10.1074/jbc.c300282200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [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: 11/06/2022] Open
Abstract
Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.
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Affiliation(s)
- Arnaud Gruez
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille, Cedex 20, France
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19
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Sulzenbacher G, Gruez A, Roig-Zamboni V, Spinelli S, Valencia C, Pagot F, Vincentelli R, Bignon C, Salomoni A, Grisel S, Maurin D, Huyghe C, Johansson K, Grassick A, Roussel A, Bourne Y, Perrier S, Miallau L, Cantau P, Blanc E, Genevois M, Grossi A, Zenatti A, Campanacci V, Cambillau C. A medium-throughput crystallization approach. Acta Crystallogr D Biol Crystallogr 2002; 58:2109-15. [PMID: 12454472 DOI: 10.1107/s0907444902013938] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2002] [Accepted: 08/05/2002] [Indexed: 11/10/2022]
Abstract
The first results of a medium-scale structural genomics program clearly demonstrate the value of using a medium-throughput crystallization approach based on a two-step procedure: a large screening step employing robotics, followed by manual or automated optimization of the crystallization conditions. The structural genomics program was based on cloning in the Gateway vectors pDEST17, introducing a long 21-residue tail at the N-terminus. So far, this tail has not appeared to hamper crystallization. In ten months, 25 proteins were subjected to crystallization; 13 yielded crystals, of which ten led to usable data sets and five to structures. Furthermore, the results using a robot dispensing 50-200 nl drops indicate that smaller protein samples can be used for crystallization. These still partial results might indicate present and future directions for those who have to make crucial choices concerning their crystallization platform in structural genomics programs.
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Affiliation(s)
- Gerlind Sulzenbacher
- AFMB, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 Chemin J Aiguier, F-13402 Marseille CEDEX 20, France
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20
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Brown K, Roig-Zamboni V, Cutruzzola' F, Arese M, Sun W, Brunori M, Cambillau C, Tegoni M. Domain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa. J Mol Biol 2001; 312:541-54. [PMID: 11563915 DOI: 10.1006/jmbi.2001.4986] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [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: 11/22/2022]
Abstract
The nitrite reductase (NIR) from Pseudomonas aeruginosa (NIR-Pa) is a soluble enzyme catalysing the reduction of nitrite (NO2(-)) to nitric oxide (NO). The enzyme is a 120 kDa homodimer, in which the monomers carry a c-heme domain and a d(1)-heme domain. The structures of the enzyme in both the oxidised and reduced state were solved previously and indicate His327 and His369 as putative catalytic residues. The kinetic characterisation of site-directed mutants has shown that the substitution of either one of these two His with Ala dramatically reduces the physiologically relevant reactivity towards nitrite, leaving the reactivity towards oxygen unaffected. The three-dimensional structures of P. aeruginosa NIR mutant H327A, and H369A in complex with NO have been solved by multiple wavelength anomalous dispersion (MAD), using the iron anomalous signal, and molecular replacement techniques. In both refined crystal structures the c-heme domain, whilst preserving its classical c-type cytochrome fold, has undergone a 60 degrees rigid-body rotation around an axis parallel with the pseudo 8-fold axis of the beta-propeller, and passing through residue Gln115. Even though the distance between the Fe ions of the c and d(1)-heme remains 21 A, the edge-to-edge distance between the two hemes has increased by 5 A. Furthermore the distal side of the d(1)-heme pocket appears to have undergone structural re-arrangement and Tyr10 has moved out of the active site. In the H369A-NO complex, the position and orientation of NO is significantly different from that of the NO bound to the reduced wild-type structure. Our results provide insight into the flexibility of the enzyme and the distinction between nitrite and oxidase reduction mechanisms. Moreover they demonstrate that the two histidine residues play a crucial role in the physiological activity of nitrite reduction, ligand binding and in the structural organisation of nitrite reductase from P. aeruginosa.
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Affiliation(s)
- K Brown
- Architecture et Fonction des Macromolécules Biologiques U.M.R.6098, C.N.R.S and Universités d'Aix-Marseille I and II, 31, Ch.Joseph Aiguier, Marseille Cedex 20, F-13402, France
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