1
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Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024; 32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAsAsp,Asn,His,Tyr for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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2
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Nguyen A, Gemmecker G, Softley CA, Movsisyan LD, Pfaffeneder T, Heine A, Reuter K, Diederich F, Sattler M, Klebe G. 19F-NMR Unveils the Ligand-Induced Conformation of a Catalytically Inactive Twisted Homodimer of tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:1745-1755. [PMID: 35763700 DOI: 10.1021/acschembio.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the structural arrangements of protein oligomers can support the design of ligands that interfere with their function in order to develop new therapeutic concepts for disease treatment. Recent crystallographic studies have elucidated a novel twisted and functionally inactive form of the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative target in the fight against shigellosis. Active-site ligands have been identified that stimulate the rearrangement of one monomeric subunit by 130° against the other one to form an inactive twisted homodimer state. To assess whether the crystallographic observations also reflect the conformation in solution and rule out effects from crystal packing, we performed 19F-NMR spectroscopy with the introduction of 5-fluorotryptophans at four sites in TGT. The inhibitor-induced conformation of TGT in solution was assessed based on 19F-NMR chemical shift perturbations. We investigated the effect of C(4) substituted lin-benzoguanine ligands and identified a correlation between dynamic protein rearrangements and ligand-binding features in the corresponding crystal structures. These involve the destabilization of a helix next to the active site and the integrity of a flexible loop-helix motif. Ligands that either completely lack an attached C(4) substituent or use it to stabilize the geometry of the functionally competent dimer state do not indicate the presence of the twisted dimer form in the NMR spectra. The perturbation of crucial structural motifs in the inhibitors correlates with an increasing formation of the inactive twisted dimer state, suggesting these ligands are able to shift a conformational equilibrium from active C2-symmetric to inactive twisted dimer conformations. These findings suggest a novel concept for the design of drug candidates for further development.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Gerd Gemmecker
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Charlotte A Softley
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Levon D Movsisyan
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Toni Pfaffeneder
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - François Diederich
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Michael Sattler
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
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3
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Sarid L, Ankri S. Are Metabolites From the Gut Microbiota Capable of Regulating Epigenetic Mechanisms in the Human Parasite Entamoeba histolytica? Front Cell Dev Biol 2022; 10:841586. [PMID: 35300430 PMCID: PMC8921869 DOI: 10.3389/fcell.2022.841586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
The unicellular parasite Entamoeba histolytica inhabits the human gut. It has to adapt to a complex environment that consists of the host microbiota, nutritional stress, oxidative stress, and nitrosative stress. Adaptation to this complex environment is vital for the survival of this parasite. Studies have shown that the host microbiota shapes virulence and stress adaptation in E. histolytica. Increasing evidence suggests that metabolites from the microbiota mediate communication between the parasite and microbiota. In this review, we discuss the bacterial metabolites that regulate epigenetic processes in E. histolytica and the implications that this knowledge may have for the development of new anti-amebic strategies.
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Affiliation(s)
- Lotem Sarid
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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4
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Sievers K, Welp L, Urlaub H, Ficner R. Structural and functional insights into human tRNA guanine transgylcosylase. RNA Biol 2021; 18:382-396. [PMID: 34241577 DOI: 10.1080/15476286.2021.1950980] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic tRNA guanine transglycosylase (TGT) is an RNA modifying enzyme incorporating queuine, a hypermodified guanine derivative, into the tRNAsAsp,Asn,His,Tyr. While both subunits of the functional heterodimer have been crystallized individually, much of our understanding of its dimer interface or recognition of a target RNA has been inferred from its more thoroughly studied bacterial homolog. However, since bacterial TGT, by incorporating queuine precursor preQ1, deviates not only in function, but as a homodimer, also in its subunit architecture, any inferences regarding the subunit association of the eukaryotic heterodimer or the significance of its unique catalytically inactive subunit are based on unstable footing. Here, we report the crystal structure of human TGT in its heterodimeric form and in complex with a 25-mer stem loop RNA, enabling detailed analysis of its dimer interface and interaction with a minimal substrate RNA. Based on a model of bound tRNA, we addressed a potential functional role of the catalytically inactive subunit QTRT2 by UV-crosslinking and mutagenesis experiments, identifying the two-stranded βEβF-sheet of the QTRT2 subunit as an additional RNA-binding motif.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany
| | - Luisa Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (Mbexc), University of Göttingen, Göttingen, Germany
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5
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Ankri S. Entamoeba histolytica-Gut Microbiota Interaction: More Than Meets the Eye. Microorganisms 2021; 9:microorganisms9030581. [PMID: 33809056 PMCID: PMC7998739 DOI: 10.3390/microorganisms9030581] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Amebiasis is a disease caused by the unicellular parasite Entamoeba histolytica. In most cases, the infection is asymptomatic but when symptomatic, the infection can cause dysentery and invasive extraintestinal complications. In the gut, E. histolytica feeds on bacteria. Increasing evidences support the role of the gut microbiota in the development of the disease. In this review we will discuss the consequences of E. histolytica infection on the gut microbiota. We will also discuss new evidences about the role of gut microbiota in regulating the resistance of the parasite to oxidative stress and its virulence.
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Affiliation(s)
- Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Haifa 31096, Israel
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6
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Nguyen A, Nguyen D, Phong Nguyen TX, Sebastiani M, Dörr S, Hernandez-Alba O, Debaene F, Cianférani S, Heine A, Klebe G, Reuter K. The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase. ACS Chem Biol 2020; 15:3021-3029. [PMID: 33166460 DOI: 10.1021/acschembio.0c00700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since it is only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each mutated variant with respect to the dimer and thermal stability or enzyme activity by applying native mass spectrometry, a thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate a strong influence of pH on the homodimer stability. Apparently, protonation of a histidine within the aromatic cluster supports the collapse of an essential structural motif within the dimer interface at slightly acidic pH.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Tran Xuan Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - François Debaene
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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7
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Busby KN, Fulzele A, Zhang D, Bennett EJ, Devaraj NK. Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-Protein Interactions. ACS Chem Biol 2020; 15:2247-2258. [PMID: 32706237 DOI: 10.1021/acschembio.0c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Throughout their cellular lifetime, RNA transcripts are bound to proteins, playing crucial roles in RNA metabolism, trafficking, and function. Despite the importance of these interactions, identifying the proteins that interact with an RNA of interest in mammalian cells represents a major challenge in RNA biology. Leveraging the ability to site-specifically and covalently label an RNA of interest using E. coli tRNA guanine transglycosylase and an unnatural nucleobase substrate, we establish the identification of RNA-protein interactions and the selective enrichment of cellular RNA in mammalian systems. We demonstrate the utility of this approach through the identification of known binding partners of 7SK snRNA via mass spectrometry. Through a minimal 4-nucleotide mutation of the long noncoding RNA HOTAIR, enzymatic biotinylation enables identification of putative HOTAIR binding partners in MCF7 breast cancer cells that suggest new potential pathways for oncogenic function. Furthermore, using RNA sequencing and qPCR, we establish that an engineered enzyme variant achieves high levels of labeling selectivity against the human transcriptome allowing for 145-fold enrichment of cellular RNA directly from mammalian cell lysates. The flexibility and breadth of this approach suggests that this system could be routinely applied to the functional characterization of RNA, greatly expanding the toolbox available for studying mammalian RNA biology.
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Affiliation(s)
- Kayla N Busby
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Amitkumar Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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8
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Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020; 21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
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Affiliation(s)
- Julia Mathlin
- Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Loredana Le Pera
- CNR-Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Teresa Colombo
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
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9
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Busby KN, Devaraj NK. Enzymatic covalent labeling of RNA with RNA transglycosylation at guanosine (RNA-TAG). Methods Enzymol 2020; 641:373-399. [PMID: 32713531 DOI: 10.1016/bs.mie.2020.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Technologies for the labeling, detection, and manipulation of biomolecules have drastically improved our understanding of cell biology. As the myriad of functional roles for RNA in the cell are increasingly recognized, such tools to enable further investigation of RNA are the subject of much interest. RNA-TAG is an enzymatic method for site-specific, covalent labeling of RNA. This methodology makes use of a bacterial tRNA modifying enzyme, tRNA guanine transglycosylase, to incorporate modified substrate analogs into a target RNA, resulting in highly efficient and site-specific RNA labeling. In this chapter, we introduce the underlying principles of the RNA labeling reaction, discuss various applications of RNA-TAG, and present protocols for labeling specific RNA transcripts using this system.
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Affiliation(s)
- Kayla N Busby
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, United States.
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10
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Yamaotsu N, Hirono S. In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery. J Comput Aided Mol Des 2018; 32:1229-1245. [PMID: 30196523 DOI: 10.1007/s10822-018-0160-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/04/2018] [Indexed: 01/09/2023]
Abstract
Here, we propose an in silico fragment-mapping method as a potential tool for fragment-based/structure-based drug discovery (FBDD/SBDD). For this method, we created a database named Canonical Subsite-Fragment DataBase (CSFDB) and developed a knowledge-based fragment-mapping program, Fsubsite. CSFDB consists of various pairs of subsite-fragments derived from X-ray crystal structures of known protein-ligand complexes. Using three-dimensional similarity-matching between subsites on one protein and another, Fsubsite compares the surface of a target protein with all subsites in CSFDB. When a local topography similar to the subsite is found on the surface, Fsubsite places a fragment combined with the subsite in CSFDB on the target protein. For validation purposes, we applied the method to the apo-structure of cyclin-dependent kinase 2 (CDK2) and identified four compounds containing three mapped fragments that existed in the list of known inhibitors of CDK2. Next, the utility of our fragment-mapping method for fragment-growing was examined on the complex structure of tRNA-guanine transglycosylase with a small ligand. Fsubsite mapped appropriate fragments on the same position as the binding ligand or in the vicinity of the ligand. Finally, a 3D-pharmacophore model was constructed from the fragments mapped on the apo-structure of heat shock protein 90-α (HSP90α). Then, 3D pharmacophore-based virtual screening was carried out using a commercially available compound database. The resultant hit compounds were very similar to a known ligand of HSP90α. As a result of these findings, this in silico fragment-mapping method seems to be a useful tool for computational FBDD and SBDD.
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Affiliation(s)
- Noriyuki Yamaotsu
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Shuichi Hirono
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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11
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Ehrmann FR, Kalim J, Pfaffeneder T, Bernet B, Hohn C, Schäfer E, Botzanowski T, Cianférani S, Heine A, Reuter K, Diederich F, Klebe G. Austausch der Proteinkontaktflächen in der homodimeren tRNA-Guanin-Transglycosylase: ein Weg der funktionellen Regulation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Jorna Kalim
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Bruno Bernet
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Christoph Hohn
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg Frankreich
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg Frankreich
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
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12
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Ehrmann FR, Kalim J, Pfaffeneder T, Bernet B, Hohn C, Schäfer E, Botzanowski T, Cianférani S, Heine A, Reuter K, Diederich F, Klebe G. Swapping Interface Contacts in the Homodimeric tRNA-Guanine Transglycosylase: An Option for Functional Regulation. Angew Chem Int Ed Engl 2018; 57:10085-10090. [DOI: 10.1002/anie.201804627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Jorna Kalim
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Bruno Bernet
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Christoph Hohn
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique; Université de Strasbourg; CNRS, IPHC UMR 7178; 67000 Strasbourg France
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3, HCI 8093 Zürich Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
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13
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Behrens C, Biela I, Petiot-Bécard S, Botzanowski T, Cianférani S, Sager CP, Klebe G, Heine A, Reuter K. Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase. Biochemistry 2018; 57:3953-3965. [DOI: 10.1021/acs.biochem.8b00294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christina Behrens
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Inna Biela
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Stéphanie Petiot-Bécard
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Christoph P. Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
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14
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Ehrmann FR, Stojko J, Metz A, Debaene F, Barandun LJ, Heine A, Diederich F, Cianférani S, Reuter K, Klebe G. Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition. PLoS One 2017; 12:e0175723. [PMID: 28419165 PMCID: PMC5395182 DOI: 10.1371/journal.pone.0175723] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/30/2017] [Indexed: 01/05/2023] Open
Abstract
For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT) is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed. Thus, soaked structures may be misleading and suggest irrelevant binding modes. Accordingly, we re-investigated these complexes by co-crystallization. The obtained structures revealed large conformational rearrangements not visible in the soaked complexes. They result from spatial perturbations in the ribose-34/phosphate-35 recognition pocket and, consequently, an extended loop-helix motif required to prevent access of water molecules into the dimer interface loses its geometric integrity. Thermodynamic profiles of ligand binding in solution indicate favorable entropic contributions to complex formation when large conformational adaptations in the dimer interface are involved. Native MS titration experiments reveal the extent to which the homodimer is destabilized in the presence of each inhibitor. Unexpectedly, one ligand causes a complete rearrangement of subunit packing within the homodimer, never observed in any other TGT crystal structure before. Likely, this novel twisted dimer is catalytically inactive and, therefore, suggests that stabilizing this non-productive subunit arrangement may be used as a further strategy for TGT inhibition.
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Affiliation(s)
| | - Johann Stojko
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - François Debaene
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | | | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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15
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Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification. Biomolecules 2017; 7:biom7010014. [PMID: 28208632 PMCID: PMC5372726 DOI: 10.3390/biom7010014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.
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16
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Neeb M, Hohn C, Ehrmann FR, Härtsch A, Heine A, Diederich F, Klebe G. Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding? Bioorg Med Chem 2016; 24:4900-4910. [DOI: 10.1016/j.bmc.2016.07.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/24/2016] [Indexed: 11/29/2022]
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17
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Hohn C, Härtsch A, Ehrmann FR, Pfaffeneder T, Trapp N, Dumele O, Klebe G, Diederich F. An Immucillin-Based Transition-State-Analogous Inhibitor of tRNA-Guanine Transglycosylase (TGT). Chemistry 2016; 22:6750-4. [PMID: 26991861 DOI: 10.1002/chem.201600883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 11/06/2022]
Abstract
Shigellosis is one of the most severe diarrheal diseases worldwide without any efficient treatment so far. The enzyme tRNA-guanine transglycosylase (TGT) has been identified as a promising target for small-molecule drug design. Herein, we report a transition-state analogue, a small, immucillin-derived inhibitor, as a new lead structure with a novel mode of action. The complex inhibitor synthesis was accomplished in 18 steps with an overall yield of 3 %. A co-crystal structure of the inhibitor bound to Z. mobilis TGT confirmed the predicted conformation of the immucillin derivative in the enzyme active site.
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Affiliation(s)
- Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Frederik Rainer Ehrmann
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Oliver Dumele
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland.
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18
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Jakobi S, Nguyen PTX, Debaene F, Cianférani S, Reuter K, Klebe G. What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt. ACS Chem Biol 2015; 10:1897-907. [PMID: 25951081 DOI: 10.1021/acschembio.5b00028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Shigella bacteria constitute the causative agent of bacillary dysentery, an acute inflammatory disease causing the death of more than one million humans per year. A null mutation in the tgt gene encoding the tRNA-modifying enzyme tRNA-guanine transglycosylase (Tgt) was found to drastically decrease the pathogenicity of Shigella bacteria, suggesting the use of Tgt as putative target for selective antibiotics. The enzyme is only functionally active as a homodimer; thus, interference with the formation of its protein-protein interface is an attractive opportunity for therapeutic intervention. To better understand the driving forces responsible for the assembly, stability, and formation of the homodimer, we studied the properties of the residues that establish the dimer interface in detail. We performed site-directed mutagenesis and controlled shifts in the monomer/dimer equilibrium ratio in solution in a concentration-dependent manner by native mass spectrometry and used crystal structure analysis to elucidate the geometrical modulations resulting from mutational variations. The wild-type enzyme exhibits nearly exclusive dimer geometry. A patch of four aromatic amino acids, embedded into a ring of hydrophobic residues and further stabilized by a network of H-bonds, is essential for the stability of the dimer's contact. Accordingly, any perturbance in the constitution of this aromatic patch by nonaromatic residues reduces dimer stability significantly, with some of these exchanges resulting in a nearly exclusively monomeric state. Apart from the aromatic hot spot, the interface comprises an extended loop-helix motif that exhibits remarkable flexibility. In the destabilized mutated variants, the loop-helix motif adopts deviating conformations in the interface region, and a number of water molecules, penetrating into the interface, are observed.
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Affiliation(s)
- Stephan Jakobi
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Phong T. X. Nguyen
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - François Debaene
- BioOrganic
Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC,
25 rue Becquerel, 67087 Strasbourg, France
- CNRS, UMR7178, 67087 Strasbourg, France
| | - Sarah Cianférani
- BioOrganic
Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC,
25 rue Becquerel, 67087 Strasbourg, France
- CNRS, UMR7178, 67087 Strasbourg, France
| | - Klaus Reuter
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
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19
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Sawhney B, Chopra K, Misra R, Ranjan A. Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies. J Biomol Struct Dyn 2015; 33:2404-20. [PMID: 25869381 DOI: 10.1080/07391102.2015.1040074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
tRNA modifications play an important role in the proper folding of tRNA and thereby determine its functionality as an adaptor molecule. Notwithstanding the centrality of this basic process in translation, a major gap in the genomics of Plasmodium falciparum is unambiguous identification of enzymes catalysing the various tRNA modifications. In this study, tRNA-modifying enzymes of P. falciparum were annotated using homology-based approach. Based on the presence of these identified enzymes, the modifications were compared with those of prokaryotic and eukaryotic organisms. Through sequence comparison and phylogenetic analysis, we have identified P. falciparum apicoplast tRNA-guanine 34 transglycosylase (TGT, EC: 2.4.2.29), which shows evidence of its prokaryotic origin. The docking analysis of the modelled TGT structures revealed that binding of quinazolinone derivatives is more favourable with P. falciparum apicoplast TGT as compared to human TGT. Molecular dynamic simulation and molecular mechanics/generalized Born surface area analysis of the complex confirmed the greater binding affinity of the ligand in the binding pocket of P. falciparum TGT protein. Further, evolutionary patterning analysis identified the amino acids of P. falciparum apicoplast TGT that are under purifying selection pressure and hence can be good inhibitor-targeting sites. Based on these computational studies, we suggest that P. falciparum apicoplast tRNA-guanine 34 transglycosylase can be a promising drug target.
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Affiliation(s)
- Bhavik Sawhney
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Kriti Chopra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,c Department of Biotechnology and Bioinformatics, School of Life Sciences , University of Hyderabad , Gachibowli, Hyderabad , Telangana 500046 , India.,d National Centre for Cell Science, NCCS Complex , University of Pune Campus , Ganeshkhind, Pune , Maharashtra 411007 , India
| | - Rohan Misra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Akash Ranjan
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India
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20
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Fergus C, Barnes D, Alqasem MA, Kelly VP. The queuine micronutrient: charting a course from microbe to man. Nutrients 2015; 7:2897-929. [PMID: 25884661 PMCID: PMC4425180 DOI: 10.3390/nu7042897] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/25/2015] [Indexed: 12/24/2022] Open
Abstract
Micronutrients from the diet and gut microbiota are essential to human health and wellbeing. Arguably, among the most intriguing and enigmatic of these micronutrients is queuine, an elaborate 7-deazaguanine derivative made exclusively by eubacteria and salvaged by animal, plant and fungal species. In eubacteria and eukaryotes, queuine is found as the sugar nucleotide queuosine within the anticodon loop of transfer RNA isoacceptors for the amino acids tyrosine, asparagine, aspartic acid and histidine. The physiological requirement for the ancient queuine molecule and queuosine modified transfer RNA has been the subject of varied scientific interrogations for over four decades, establishing relationships to development, proliferation, metabolism, cancer, and tyrosine biosynthesis in eukaryotes and to invasion and proliferation in pathogenic bacteria, in addition to ribosomal frameshifting in viruses. These varied effects may be rationalized by an important, if ill-defined, contribution to protein translation or may manifest from other presently unidentified mechanisms. This article will examine the current understanding of queuine uptake, tRNA incorporation and salvage by eukaryotic organisms and consider some of the physiological consequence arising from deficiency in this elusive and lesser-recognized micronutrient.
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Affiliation(s)
- Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Dominic Barnes
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Mashael A Alqasem
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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21
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Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crécy-Lagard V. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol 2014; 9:1812-25. [PMID: 24911101 PMCID: PMC4136680 DOI: 10.1021/cb500278k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Queuosine (Q) is a modification found
at the wobble position of
tRNAs with GUN anticodons. Although Q is present in most eukaryotes
and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or
microflora, making q an important but under-recognized micronutrient
for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases
(eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous
accessory subunit (QTRTD1) forming a complex that catalyzes q insertion
into target tRNAs. Phylogenetic analysis of eTGT subunits revealed
a patchy distribution pattern in which gene losses occurred independently
in different clades. Searches for genes co-distributing with eTGT
family members identified DUF2419 as a potential Q salvage protein
family. This prediction was experimentally validated in Schizosaccharomyces
pombe by confirming that Q was present by analyzing tRNAAsp with anticodon GUC purified from wild-type cells and by
showing that Q was absent from strains carrying deletions in the QTRT1
or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya
with a few possible cases of horizontal gene transfer to bacteria.
The universality of the DUF2419 function was confirmed by complementing
the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues.
The enzymatic function of this family is yet to be determined, but
structural similarity with DNA glycosidases suggests a ribonucleoside
hydrolase activity.
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Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Céline Brochier-Armanet
- Université
Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie
Evolutive, Université de Lyon, 69622 Villeurbanne, France
| | - Kirk W. Gaston
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Farhad Forouhar
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - John F. Hunt
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Genetics Institute, Gainesville, Florida 32611, United States
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22
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Jakobi S, Nguyen TXP, Debaene F, Metz A, Sanglier-Cianférani S, Reuter K, Klebe G. Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme. Proteins 2014; 82:2713-32. [DOI: 10.1002/prot.24637] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/24/2014] [Accepted: 06/18/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Stephan Jakobi
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg; Marbacher Weg 6 D-35032 Marburg Germany
| | - Tran Xuan Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg; Marbacher Weg 6 D-35032 Marburg Germany
| | - François Debaene
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg; CNRS UMR7178; 25 rue Becquerel 67087 Strasbourg France
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg; Marbacher Weg 6 D-35032 Marburg Germany
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg; CNRS UMR7178; 25 rue Becquerel 67087 Strasbourg France
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg; Marbacher Weg 6 D-35032 Marburg Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg; Marbacher Weg 6 D-35032 Marburg Germany
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23
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Neeb M, Betz M, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G. Beyond Affinity: Enthalpy–Entropy Factorization Unravels Complexity of a Flat Structure–Activity Relationship for Inhibition of a tRNA-Modifying Enzyme. J Med Chem 2014; 57:5566-78. [DOI: 10.1021/jm5006868] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Neeb
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Michael Betz
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Luzi Jakob Barandun
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Christoph Hohn
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - François Diederich
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
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24
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Neeb M, Czodrowski P, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G. Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme. J Med Chem 2014; 57:5554-65. [PMID: 24955548 DOI: 10.1021/jm500401x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Drug molecules should remain uncharged while traveling through the body and crossing membranes and should only adopt charged state upon protein binding, particularly if charge-assisted interactions can be established in deeply buried binding pockets. Such strategy requires careful pKa design and methods to elucidate whether and where protonation-state changes occur. We investigated the protonation inventory in a series of lin-benzoguanines binding to tRNA-guanine transglycosylase, showing pronounced buffer dependency during ITC measurements. Chemical modifications of the parent scaffold along with ITC measurements, pKa calculations, and site-directed mutagenesis allow elucidating the protonation site. The parent scaffold exhibits two guanidine-type portions, both likely candidates for proton uptake. Even mutually compensating effects resulting from proton release of the protein and simultaneous uptake by the ligand can be excluded. Two adjacent aspartates induce a strong pKa shift at the ligand site, resulting in protonation-state transition. Furthermore, an array of two parallel H-bonds avoiding secondary repulsive effects contributes to the high-affinity binding of the lin-benzoguanines.
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Affiliation(s)
- Manuel Neeb
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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25
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Eichhorn CD, Kang M, Feigon J. Structure and function of preQ 1 riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:939-950. [PMID: 24798077 DOI: 10.1016/j.bbagrm.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022]
Abstract
PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Mijeong Kang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
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26
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Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One 2013; 8:e75992. [PMID: 24098414 PMCID: PMC3787967 DOI: 10.1371/journal.pone.0075992] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/13/2013] [Indexed: 12/19/2022] Open
Abstract
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.
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Affiliation(s)
- Ryan G. Coleman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael Carchia
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Teague Sterling
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John J. Irwin
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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27
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Barandun LJ, Immekus F, Kohler PC, Ritschel T, Heine A, Orlando P, Klebe G, Diederich F. High-affinity inhibitors ofZymomonas mobilistRNA–guanine transglycosylase through convergent optimization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1798-807. [DOI: 10.1107/s0907444913014509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/26/2013] [Indexed: 11/11/2022]
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Immekus F, Barandun LJ, Betz M, Debaene F, Petiot S, Sanglier-Cianferani S, Reuter K, Diederich F, Klebe G. Launching spiking ligands into a protein-protein interface: a promising strategy to destabilize and break interface formation in a tRNA modifying enzyme. ACS Chem Biol 2013; 8:1163-78. [PMID: 23534552 DOI: 10.1021/cb400020b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apart from competitive active-site inhibition of protein function, perturbance of protein-protein interactions by small molecules in oligodomain enzymes opens new perspectives for innovative therapeutics. tRNA-guanine transglycosylase (TGT), a potential target to treat shigellosis, is active only as the homodimer. Consequently, disruption of the dimer interface by small molecules provides a novel inhibition mode. A special feature of this enzyme is the short distance between active site and rim of the dimer interface. This suggests design of expanded active-site inhibitors decorated with rigid, needle-type substituents to spike into potential hot spots of the interaction interface. Ligands with attached ethinyl-type substituents have been synthesized and characterized by Kd measurements, crystallography, noncovalent mass spectrometry, and computer simulations. In contrast to previously determined crystal structures with nonextended active-site inhibitors, a well-defined loop-helix motif, involved in several contacts across the dimer interface, falls apart and suggests enhanced flexibility once the spiking ligands are bound. Mass spectrometry indicates significant destabilization but not full disruption of the complexed TGT homodimer in solution. As directed interactions of the loop-helix motif obviously do not determine dimer stability, a structurally conserved hydrophobic patch composed of several aromatic amino acids is suggested as interaction hot spot. The residues of this patch reside on a structurally highly conserved helix-turn-helix motif, which remains unaffected by the bound spiking ligands. Nevertheless, it is shielded from solvent access by the loop-helix motif that becomes perturbed upon binding of the spiking ligands, which serves as a possible explanation for reduced interface stability.
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Affiliation(s)
- Florian Immekus
- Institut für Pharmazeutische
Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Luzi Jakob Barandun
- Laboratorium für Organische
Chemie, ETH Zurich Hönggerberg, HCI, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Michael Betz
- Institut für Pharmazeutische
Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Debaene
- Laboratoire de Spectrométrie de Masse Bio-Organique de Strasbourg, 25, rue Becquerel,
67087 Strasbourg Cedex 2, France
| | - Stéphanie Petiot
- Laboratoire de Spectrométrie de Masse Bio-Organique de Strasbourg, 25, rue Becquerel,
67087 Strasbourg Cedex 2, France
| | - Sarah Sanglier-Cianferani
- Laboratoire de Spectrométrie de Masse Bio-Organique de Strasbourg, 25, rue Becquerel,
67087 Strasbourg Cedex 2, France
| | - Klaus Reuter
- Institut für Pharmazeutische
Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Diederich
- Laboratorium für Organische
Chemie, ETH Zurich Hönggerberg, HCI, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institut für Pharmazeutische
Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Lounnas V, Ritschel T, Kelder J, McGuire R, Bywater RP, Foloppe N. Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery. Comput Struct Biotechnol J 2013; 5:e201302011. [PMID: 24688704 PMCID: PMC3962124 DOI: 10.5936/csbj.201302011] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/26/2013] [Accepted: 02/08/2013] [Indexed: 12/20/2022] Open
Abstract
The past decade has witnessed a paradigm shift in preclinical drug discovery with structure-based drug design (SBDD) making a comeback while high-throughput screening (HTS) methods have continued to generate disappointing results. There is a deficit of information between identified hits and the many criteria that must be fulfilled in parallel to convert them into preclinical candidates that have a real chance to become a drug. This gap can be bridged by investigating the interactions between the ligands and their receptors. Accurate calculations of the free energy of binding are still elusive; however progresses were made with respect to how one may deal with the versatile role of water. A corpus of knowledge combining X-ray structures, bioinformatics and molecular modeling techniques now allows drug designers to routinely produce receptor homology models of increasing quality. These models serve as a basis to establish and validate efficient rationales used to tailor and/or screen virtual libraries with enhanced chances of obtaining hits. Many case reports of successful SBDD show how synergy can be gained from the combined use of several techniques. The role of SBDD with respect to two different classes of widely investigated pharmaceutical targets: (a) protein kinases (PK) and (b) G-protein coupled receptors (GPCR) is discussed. Throughout these examples prototypical situations covering the current possibilities and limitations of SBDD are presented.
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Affiliation(s)
- Valère Lounnas
- CMBI, NCMLS Radboud University, Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Tina Ritschel
- Computational Drug Discovery, CMBI, NCMLS, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Jan Kelder
- Beethovengaarde 97, 5344 CD Oss, The Netherlands
| | - Ross McGuire
- BioAxis Research BV, Pivot Park, Molenstraat 110, 5342 CC Oss, The Netherlands
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30
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Struktur und Funktion nicht-kanonischer Nukleobasen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Structure and function of noncanonical nucleobases. Angew Chem Int Ed Engl 2012; 51:7110-31. [PMID: 22744788 DOI: 10.1002/anie.201201193] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/07/2012] [Indexed: 12/19/2022]
Abstract
DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m(5) dC, hm(5) dC, f(5) dC und ca(5) dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell-type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non-canonical nucleosides in both DNA and RNA.
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Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany.
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32
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Barandun LJ, Immekus F, Kohler PC, Tonazzi S, Wagner B, Wendelspiess S, Ritschel T, Heine A, Kansy M, Klebe G, Diederich F. From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters. Chemistry 2012; 18:9246-57. [PMID: 22736391 DOI: 10.1002/chem.201200809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Indexed: 11/12/2022]
Abstract
The foodborne illness shigellosis is caused by Shigella bacteria that secrete the highly cytotoxic Shiga toxin, which is also formed by the closely related enterohemorrhagic Escherichia coli (EHEC). It has been shown that tRNA-guanine transglycosylase (TGT) is essential for the pathogenicity of Shigella flexneri. Herein, the molecular recognition properties of a guanine binding pocket in Zymomonas mobilis TGT are investigated with a series of lin-benzohypoxanthine- and lin-benzoguanine-based inhibitors that bear substituents to occupy either the ribose-33 or the ribose-34 pocket. The three inhibitor scaffolds differ by the substituent at C(6) being H, NH(2), or NH-alkyl. These differences lead to major changes in the inhibition constants, pK(a) values, and binding modes. Compared to the lin-benzoguanines, with an exocyclic NH(2) at C(6), the lin-benzohypoxanthines without an exocyclic NH(2) group have a weaker affinity as several ionic protein-ligand hydrogen bonds are lost. X-ray cocrystal structure analysis reveals that a new water cluster is imported into the space vacated by the lacking NH(2) group and by a conformational shift of the side chain of catalytic Asp102. In the presence of an N-alkyl group at C(6) in lin-benzoguanine ligands, this water cluster is largely maintained but replacement of one of the water molecules in the cluster leads to a substantial loss in binding affinity. This study provides new insight into the role of water clusters at enzyme active sites and their challenging substitution by ligand parts, a topic of general interest in contemporary structure-based drug design.
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Affiliation(s)
- Luzi Jakob Barandun
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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33
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Kirchmair J, Spitzer GM, Liedl KR. Consideration of Water and Solvation Effects in Virtual Screening. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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34
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Chen YC, Brooks AF, Goodenough-Lashua DM, Kittendorf JD, Showalter HD, Garcia GA. Evolution of eukaryal tRNA-guanine transglycosylase: insight gained from the heterocyclic substrate recognition by the wild-type and mutant human and Escherichia coli tRNA-guanine transglycosylases. Nucleic Acids Res 2010; 39:2834-44. [PMID: 21131277 PMCID: PMC3074131 DOI: 10.1093/nar/gkq1188] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The enzyme tRNA-guanine transglycosylase (TGT) is involved in the queuosine modification of tRNAs in eukarya and eubacteria and in the archaeosine modification of tRNAs in archaea. However, the different classes of TGTs utilize different heterocyclic substrates (and tRNA in the case of archaea). Based on the X-ray structural analyses, an earlier study [Stengl et al. (2005) Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism. Chembiochem, 6, 1926–1939] has made a compelling case for the divergent evolution of the eubacterial and archaeal TGTs. The X-ray structure of the eukaryal class of TGTs is not known. We performed sequence homology and phylogenetic analyses, and carried out enzyme kinetics studies with the wild-type and mutant TGTs from Escherichia coli and human using various heterocyclic substrates that we synthesized. Observations with the Cys145Val (E. coli) and the corresponding Val161Cys (human) TGTs are consistent with the idea that the Cys145 evolved in eubacterial TGTs to recognize preQ1 but not queuine, whereas the eukaryal equivalent, Val161, evolved for increased recognition of queuine and a concomitantly decreased recognition of preQ1. Both the phylogenetic and kinetic analyses support the conclusion that all TGTs have divergently evolved to specifically recognize their cognate heterocyclic substrates.
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Affiliation(s)
- Yi-Chen Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
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35
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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36
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Chen YC, Kelly VP, Stachura SV, Garcia GA. Characterization of the human tRNA-guanine transglycosylase: confirmation of the heterodimeric subunit structure. RNA (NEW YORK, N.Y.) 2010; 16:958-68. [PMID: 20354154 PMCID: PMC2856889 DOI: 10.1261/rna.1997610] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 02/09/2010] [Indexed: 05/21/2023]
Abstract
The eukaryotic tRNA-guanine transglycosylase (TGT) has been reported to exist as a heterodimer, in contrast to the homodimeric eubacterial TGT. While ubiquitin-specific protease 14 (USP14) has been proposed to act as a regulatory subunit of the eukaryotic TGT, the mouse TGT has recently been shown to be a queuine tRNA-ribosyltransferase 1 (QTRT1, eubacterial TGT homolog).queuine tRNA-ribosyltransferase domain-containing 1 (QTRTD1) heterodimer. We find that human QTRTD1 (hQTRTD1) co-purifies with polyhistidine-tagged human QTRT1 (ht-hQTRT1) via Ni(2+) affinity chromatography. Cross-linking experiments, mass spectrometry, and size exclusion chromatography results are consistent with the two proteins existing as a heterodimer. We have not been able to observe co-purification and/or association between hQTRT1 and USP14 when co-expressed in Escherichia coli. More importantly, under our experimental conditions, the transglycosylase activity of hQTRT1 is only observed when hQTRT1 and hQTRTD1 have been co-expressed and co-purified. Kinetic characterization of the human TGT (hQTRT1.hQTRTD1) using human tRNA(Tyr) and guanine shows catalytic efficiency (k(cat)/K(M)) similar to that of the E. coli TGT. Furthermore, site-directed mutagenesis confirms that the hQTRT1 subunit is responsible for the transglycosylase activity. Taken together, these results indicate that the human TGT is composed of a catalytic subunit, hQTRT1, and hQTRTD1, not USP14. hQTRTD1 has been implicated as the salvage enzyme that generates free queuine from QMP. Work is ongoing in our laboratory to confirm this activity.
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Affiliation(s)
- Yi-Chen Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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37
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Ritschel T, Kohler PC, Neudert G, Heine A, Diederich F, Klebe G. How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase. ChemMedChem 2010; 4:2012-23. [PMID: 19894214 DOI: 10.1002/cmdc.200900343] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In a computational and structural study, we investigated a series of 4-substituted lin-benzoguanines that are potent inhibitors of tRNA-guanine transglycosylase (TGT), a putative target for the treatment of shigellosis. At first glance, it appears self-evident that the placement of a positively charged ligand functional group between the carboxylate groups of two adjacent aspartate residues in the glycosylase catalytic center leads to enhanced ligand binding. The concomitant displacement of water molecules that partially solvate the aspartates prior to ligand binding appears to result as a consequence of this. However, the case study presented herein shows that this premise is much too superficial. Placement of a likely positively charged amino group at such a pivotal position, interfering with the residual water solvation shell, is at best cost-neutral compared with the unsubstituted parent ligand not conflicting with the residual water shell. A ligand that orients a hydroxy group in this position shows even decreased binding. Based on the cost-neutral placement of the amino functionality, hydrophobic side chains can now be further attached to fill, with increasing potency, a small hydrophobic pocket remote to the aspartates. Any attempts to cross the pivotal position between both aspartates with nonpolar scaffolds reveals only decreased binding, even though the waters of the residual solvation shell are successfully repelled. This surprising observation fostered a detailed analysis of the role of water molecules involved in the residual solvation of polar active site residues. Their geometry and putative replacement in the binding pocket of TGT has been studied by a comparative database analysis, computational active site mapping, and a series of crystal structure analyses. Furthermore, conformational preferences of attached hydrophobic moieties explain their contribution to a gradual increase in binding affinity.
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Affiliation(s)
- Tina Ritschel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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38
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Ritschel T, Atmanene C, Reuter K, Van Dorsselaer A, Sanglier-Cianferani S, Klebe G. An Integrative Approach Combining Noncovalent Mass Spectrometry, Enzyme Kinetics and X-ray Crystallography to Decipher Tgt Protein-Protein and Protein-RNA Interaction. J Mol Biol 2009; 393:833-47. [DOI: 10.1016/j.jmb.2009.07.040] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/06/2009] [Accepted: 07/14/2009] [Indexed: 11/29/2022]
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39
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Kohler P, Ritschel T, Schweizer W, Klebe G, Diederich F. High-Affinity Inhibitors of tRNA-Guanine Transglycosylase Replacing the Function of a Structural Water Cluster. Chemistry 2009; 15:10809-17. [DOI: 10.1002/chem.200901270] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Ritschel T, Hoertner S, Heine A, Diederich F, Klebe G. Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT. Chembiochem 2009; 10:716-27. [PMID: 19199329 DOI: 10.1002/cbic.200800782] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A novel ligand series is presented to inhibit tRNA-guanine transglycosylase (TGT), a protein with a significant role in the pathogenicity mechanism of Shigella flexneri, the causative agent of Shigellosis. The enzyme exchanges guanine in the wobble position of tRNA(Asn,Asp,His,Tyr) against a modified base. To prevent the base-exchange reaction, several series of inhibitors have already been designed, synthesized, and tested. One aim of previous studies was to address a hydrophobic pocket with different side chains attached to the parent skeletons. Disappointingly, no significant increase in binding affinity could be observed that could be explained by the disruption of a conserved water cluster. The ligand series examined in this study are based on the known scaffold lin-benzoguanine. Different side chains were introduced leading to 2-amino-lin-benzoguanines, which address a different pocket of the protein and avoid disruption of the water cluster. With the introduction of an amino group in the 2-position, a dramatic increase in binding affinity can be experienced. To explain this significant gain in binding affinity, Poisson-Boltzmann calculations were performed to explore pK(a) changes of ligand functional groups upon protein binding, they can differ significantly on going from aqueous solution to protein environment. For all complexes, a permanent protonation of the newly designed ligands is suggested, leading to a charge-assisted hydrogen bond in the protein-ligand complex. This increased strength in hydrogen bonding takes beneficial effect on binding affinity of the ligands, resulting in low-nanomolar binders. Crystal structures and docking emphasize the importance of the newly created charge-assisted hydrogen bond. A detailed analysis of the crystal structures in complex with substituted 2-amino-lin-benzoguanines indicate pronounced disorder of the attached side chains addressing the ribose 33 binding pocket. Docking suggests multiple orientations of these side chains. Obviously, an entropic advantage of the residual mobility experienced by these ligands in the bound state is beneficial and reveals an overall improved protein binding.
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Affiliation(s)
- Tina Ritschel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, Marburg, Germany
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41
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Kang M, Peterson R, Feigon J. Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell 2009; 33:784-90. [PMID: 19285444 DOI: 10.1016/j.molcel.2009.02.019] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 02/18/2009] [Accepted: 02/25/2009] [Indexed: 12/27/2022]
Abstract
The modified nucleotide queuosine (Q) is almost universally found in the anticodon wobble position of specific tRNAs. In many bacteria, biosynthesis of Q is modulated by a class of regulatory mRNA elements called riboswitches. The preQ(1) riboswitch, found in the 5'UTR of bacterial genes involved in synthesis of the Q precursors preQ(0) and preQ(1), contains the smallest known aptamer domain. We report the solution structure of the preQ(1) riboswitch aptamer domain from Bacillus subtilis bound to preQ(1), which is a unique compact pseudoknot with three loops and two stems that encapsulates preQ(1) at the junction between the two stems. The pseudoknot only forms in the presence of preQ(1), and the 3' A-rich tail of the aptamer domain is an integral part of the pseudoknot. In the absence of preQ(1), the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ(1) biosynthesis.
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Affiliation(s)
- Mijeong Kang
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
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42
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Carneiro ACD, Fragel-Madeira L, Silva-Neto MA, Linden R. A role for CK2 upon interkinetic nuclear migration in the cell cycle of retinal progenitor cells. Dev Neurobiol 2008; 68:620-31. [PMID: 18278803 DOI: 10.1002/dneu.20613] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In developing retina, the nucleus of the elongated neuroepithelial cells undergoes interkinetic nuclear migration (INM), that is it migrates back and forth across the proliferative layer during the cell cycle. S-phase occurs at the basal side, while M-phase occurs at the apical margin of the retinal progenitors. G1 and G2-phases occur along the nuclear migration pathway. We tested whether this feature of the retinal cell cycle is controlled by CK2, which, among its many substrates, phosphorylates both molecular motors and cytoskeletal components. Double immunolabeling showed that CK2 is contained in BrdU-labeled retinal progenitors. INM was examined after pulse labeling the retina of newborn rats with BrdU, by plotting nuclear movement from basal to apical sides of the retinal progenitors during G2. The CK2 specific inhibitor 4,5,6,7-tetrabromobenzotriazole inhibited the activity of rat retinal CK2, and blocked nuclear movement proper in a dose-dependent way. No apoptosis was detected, and total numbers of BrdU-labeled nuclei remained constant following treatment. Immunohistochemistry showed that, following inhibition of CK2, the tubulin cytoskeleton is disorganized, with reduced acetylated and increased tyrosinated tubulin. This indicates a reduction in stable microtubules, with accumulation of free tubulin dimers. The results show that CK2 activity is required for INM in retinal progenitor cells.
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Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
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Hörtner SR, Ritschel T, Stengl B, Kramer C, Schweizer WB, Wagner B, Kansy M, Klebe G, Diederich F. Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding. Angew Chem Int Ed Engl 2008; 46:8266-9. [PMID: 17902085 DOI: 10.1002/anie.200702961] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Simone R Hörtner
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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Hörtner S, Ritschel T, Stengl B, Kramer C, Schweizer W, Wagner B, Kansy M, Klebe G, Diederich F. Hochaffine Inhibitoren der tRNA-Guanin-Transglycosylase, eines Schlüsselenzyms in der Pathogenese der Shigellen-Ruhr: ladungsverstärkte Wasserstoffbrücken. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies. J Mol Biol 2007; 374:764-76. [PMID: 17949745 DOI: 10.1016/j.jmb.2007.09.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 09/17/2007] [Accepted: 09/21/2007] [Indexed: 11/22/2022]
Abstract
Bacterial tRNA-guanine transglycosylase (Tgt) catalyses the exchange of guanine in the wobble position of particular tRNAs by the modified base preQ(1). In vitro, however, the enzyme is also able to insert the immediate biosynthetic precursor, preQ(0), into those tRNAs. This substrate promiscuity is based on a peptide switch in the active site, gated by the general acid/base Glu235. The switch alters the properties of the binding pocket to allow either the accommodation of guanine or preQ(1). The peptide conformer recognising guanine, however, is also able to bind preQ(0). To investigate selectivity regulation, kinetic data for Zymomonas mobilis Tgt were recorded. They show that selectivity in favour of the actual substrate preQ(1) over preQ(0) is not achieved by a difference in affinity but via a higher turnover rate. Moreover, a Tgt(Glu235Gln) variant was constructed. The mutation was intended to stabilise the peptide switch in the conformation favouring guanine and preQ(0) binding. Kinetic characterisation of the mutated enzyme revealed that the Glu235Gln exchange has, with respect to all substrate bases, no significant influence on k(cat). In contrast, K(M)(preQ(1)) is drastically increased, while K(M)(preQ(0)) seems to be decreased. Hence, regarding k(cat)/K(M) as an indicator for catalytic efficiency, selectivity of Tgt in favour of preQ(1) is abolished or even inverted in favour of preQ(0) for Tgt(Glu235Gln). Crystal structures of the mutated enzyme confirm that the mutation strongly favours the binding pocket conformation required for the accommodation of guanine and preQ(0). The way this is achieved, however, significantly differs from that predicted based on crystal structures of wild-type Tgt.
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Hurt JK, Olgen S, Garcia GA. Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro. Nucleic Acids Res 2007; 35:4905-13. [PMID: 17626052 PMCID: PMC1950534 DOI: 10.1093/nar/gkm473] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 05/15/2007] [Accepted: 05/29/2007] [Indexed: 11/18/2022] Open
Abstract
Shigella flexneri is an enteropathogen responsible for severe dysentery in humans. VirF is a key transcriptional regulator that activates the expression of the downstream virulence factors required for cellular invasion and cell-to-cell spread of this pathogen. There are several environmental factors that induce the translation of VirF including temperature, pH, osmolarity and post-transcriptional RNA modification. Durand and colleagues (vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase of Escherichia coli K-12. J. Bacteriol., 176, 4627-4634) have demonstrated a correlation between VirF and tRNA-guanine transglycosylase (TGT), which catalyzes the exchange of the hypermodified base queuine for the guanine in the wobble position of certain tRNAs. They characterized tgt- mutant S. flexneri strains in which the translation of VirF is markedly reduced and the bacteria are unable to invade host cells. Although the function of TGT is to modify tRNA, we report that the virF mRNA is recognized by the Escherichia coli TGT (99% identity to the S. flexneri TGT) in vitro. Further, we show that this recognition results in the site-specific modification of a single base in the virF mRNA. In the context of previous reports that small molecule binding motifs ('riboswitches') in mRNAs modulate mRNA conformation and translation, our observations suggest that TGT may modulate the translation of VirF by base modification of the VirF encoding mRNA.
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Affiliation(s)
- Julie K. Hurt
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065 and Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, TR-06100, Ankara, Turkey
| | - Sureyya Olgen
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065 and Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, TR-06100, Ankara, Turkey
| | - George A. Garcia
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065 and Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, TR-06100, Ankara, Turkey
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