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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. THE NEW PHYTOLOGIST 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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2
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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3
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Prasanna D, Runthala A. Computationally Decoding NudF Residues To Enhance the Yield of the DXP Pathway. ACS OMEGA 2022; 7:19898-19912. [PMID: 35721994 PMCID: PMC9202048 DOI: 10.1021/acsomega.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Terpenoids form a large pool of highly diverse organic compounds possessing several economically important properties, including nutritional, aromatic, and pharmacological properties. The 1-deoxy-d-xylulose 5-phosphate (DXP) pathway's end enzyme, nuclear distribution protein (NudF), interacting with isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), is critical for the synthesis of isoprenol/prenol/downstream compounds. The enzyme is yet to be thoroughly investigated to increase the overall yield of terpenoids in the Bacillus subtilis, which is widely used in industry and is generally regarded as a safe (GRAS) bacterium. The study aims to analyze the evolutionary conservation across the active site for mapping the key residues for mutagenesis studies. The 37-sequence data set, extracted from 103 Bacillus subtilis entries, shows a high phylogenetic divergence, and only six one-motif sequences ASB92783.1, ASB69297.1, ASB56714.1, AOR97677.1, AOL97023.1, and OAZ71765.1 show a monophyly relationship, unlike a complete polyphyly relationship between the other 31 three-motif sequences. Furthermore, only 47 of 179 residues of the representative sequence CUB50584.1 are observed to be significantly conserved. Docking analysis suggests a preferential bias of adenosine diphosphate (ADP)-ribose pyrophosphatase toward IPP, and a nearly threefold energetic difference is observed between IPP and DMAPP. The loops are hereby shown to play a regulatory role in guiding the promiscuity of NudF toward a specific ligand. Computational saturation mutagenesis of the seven hotspot residues identifies two key positions LYS78 and PHE116, orderly encoded within loop1 and loop7, majorly interacting with the ligands DMAPP and IPP, and their mutants K78I/K78L and PHE116D/PHE116E are found to stabilize the overall conformation. Molecular dynamics analysis shows that the IPP complex is significantly more stable than the DMAPP complex, and the NudF structure is very unstable. Besides showing a promiscuous binding of NudF with ligands, the analysis suggests its rate-limiting nature. The study would allow us to customize the metabolic load toward the synthesis of any of the downstream molecules. The findings would pave the way for the development of catalytically improved NudF mutants for the large-scale production of specific terpenoids with significant nutraceutical or commercial value.
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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5
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Gattkowski E, Rutherford TJ, Möckl F, Bauche A, Sander S, Fliegert R, Tidow H. Analysis of ligand binding and resulting conformational changes in pyrophosphatase NUDT9. FEBS J 2021; 288:6769-6782. [PMID: 34189846 PMCID: PMC7612441 DOI: 10.1111/febs.16097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/04/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
Nudix hydrolase 9 (NUDT9) is a member of the nucleoside linked to another moiety X (NUDIX) protein superfamily, which hydrolyses a broad spectrum of organic pyrophosphates from metabolic processes. ADP‐ribose (ADPR) has been the only known endogenous substrate accepted by NUDT9 so far. The Ca2+‐permeable transient receptor potential melastatin subfamily 2 (TRPM2) channel contains a homologous NUDT9‐homology (NUDT9H) domain and is activated by ADPR. Sustained Ca2+ influx via ADPR‐activated TRPM2 triggers apoptotic mechanisms. Thus, a precise regulation of cellular ADPR levels by NUDT9 is essential. A detailed characterization of the enzyme‐substrate interaction would help to understand the high substrate specificity of NUDT9. Here, we analysed ligand binding to NUDT9 using a variety of biophysical techniques. We identified 2′‐deoxy‐ADPR as an additional substrate for NUDT9. Similar enzyme kinetics and binding affinities were determined for the two ligands. The high‐affinity binding was preserved in NUDT9 containing the mutated NUDIX box derived from the human NUDT9H domain. NMR spectroscopy indicated that ADPR and 2′‐deoxy‐ADPR bind to the same binding site of NUDT9. Backbone resonance assignment and subsequent molecular docking allowed further characterization of the binding pocket. Substantial conformational changes of NUDT9 upon ligand binding were observed which might allow for the development of NUDT9‐based ADPR fluorescence resonance energy transfer sensors that may help with the analysis of ADPR signalling processes in cells in the future.
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Affiliation(s)
- Ellen Gattkowski
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | | | - Franziska Möckl
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Andreas Bauche
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Simon Sander
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Ralf Fliegert
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
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6
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Two Decades of Evolution of Our Understanding of the Transient Receptor Potential Melastatin 2 (TRPM2) Cation Channel. Life (Basel) 2021; 11:life11050397. [PMID: 33925466 PMCID: PMC8145809 DOI: 10.3390/life11050397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
The transient receptor potential melastatin (TRPM) family belongs to the superfamily of TRP ion channels. It consists of eight family members that are involved in a plethora of cellular functions. TRPM2 is a homotetrameric Ca2+-permeable cation channel activated upon oxidative stress and is important, among others, for body heat control, immune cell activation and insulin secretion. Invertebrate TRPM2 proteins are channel enzymes; they hydrolyze the activating ligand, ADP-ribose, which is likely important for functional regulation. Since its cloning in 1998, the understanding of the biophysical properties of the channel has greatly advanced due to a vast number of structure–function studies. The physiological regulators of the channel have been identified and characterized in cell-free systems. In the wake of the recent structural biochemistry revolution, several TRPM2 cryo-EM structures have been published. These structures have helped to understand the general features of the channel, but at the same time have revealed unexplained mechanistic differences among channel orthologues. The present review aims at depicting the major research lines in TRPM2 structure-function. It discusses biophysical properties of the pore and the mode of action of direct channel effectors, and interprets these functional properties on the basis of recent three-dimensional structural models.
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Zong G, Jork N, Hostachy S, Fiedler D, Jessen HJ, Shears SB, Wang H. New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J 2021; 35:e21275. [PMID: 33475202 DOI: 10.1096/fj.202001489r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 11/11/2022]
Abstract
Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study, we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogs ("PCP-InsPs"). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as "suspension cables." We demonstrate functionality for a triglycine peptide within a β-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis, we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP6 as an inhibitor of catalytic activity.
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Affiliation(s)
- Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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8
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Taxon ES, Halbers LP, Parsons SM. Kinetics aspects of Gamma-hydroxybutyrate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2020; 1868:140376. [PMID: 31981617 DOI: 10.1016/j.bbapap.2020.140376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/22/2019] [Accepted: 01/19/2020] [Indexed: 11/18/2022]
Abstract
Two groups of metabolically related enzymes, the Group III family of Fe2+-dependent alcohol dehydrogenases (ADHs) and the separate subfamily of nucleoside diphosphates linked to x (nudix) hydrolases that activate Group III ADHs are under-characterized. Here we report the steady-state initial-velocity forward direction (alcohol → aldehyde) reaction of a Group III ADH, namely gamma-hydroxybutyrate dehydrogenase (GHBDH, UniProt: Q59104), cloned from Cupriavidus necator as a fusion protein. We also report the effects of nudix hydrolases on the GHBDH reaction. At optimal pH 9.0, the GHBDH reaction is activated ~2-fold by two different saturating purified nudix hydrolases, namely Bacillus methanolicus activator (ACT, UniProt: I3EA59) and Escherichia coli NudF (UniProt Q93K97) proteins. At physiological pH values of ~7.0, ACT activates by >3.5-fold. Initial-rate characterization at pH 9.0 of the forward direction un-activated and ACT-activated reactions show for both cases competitive inhibition by the product succinic semialdehyde versus GHB, and noncompetitive inhibitions by the three other substrate-product combinations. This pattern is consistent with NAD+ binding first in Mono-Iso Theorell-Chance kinetics. Mutants of some possibly important residues in GHBDH also were characterized. H265, conserved among all Group III ADHs and previously proposed to be a critical general base, is only ~4-fold helpful for GHBDH activity relevant to H265A. The four previously proposed conserved Fe2+ chelators (D193, H197, H261 and H280) each are essential for GHBDH activity. A 2-step explanation for cross-species stimulation by sub-stoichiometric ACT in the forward direction and confirmed lack of ACT stimulation in the reverse direction reaction is proposed.
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Affiliation(s)
- Esther S Taxon
- Department of Chemistry and Biochemistry, Department of Biomolecular Science and Engineering, University of California, Santa Barbara, California, United States
| | - Lila P Halbers
- Department of Chemistry and Biochemistry, Department of Biomolecular Science and Engineering, University of California, Santa Barbara, California, United States
| | - Stanley M Parsons
- Department of Chemistry and Biochemistry, Department of Biomolecular Science and Engineering, University of California, Santa Barbara, California, United States.
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9
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Schumacher MA, Henderson M, Zeng W. Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2020; 26:69-82. [PMID: 31704716 PMCID: PMC6913127 DOI: 10.1261/rna.072231.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5' end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase, we determined structures of apo, GTP-bound and RNA-bound T. brucei MERS1 to 2.30 Å, 2.45 Å, and 2.60 Å, respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single-stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2-like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate-binding activities.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Max Henderson
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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10
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Iordanov I, Tóth B, Szollosi A, Csanády L. Enzyme activity and selectivity filter stability of ancient TRPM2 channels were simultaneously lost in early vertebrates. eLife 2019; 8:44556. [PMID: 30938679 PMCID: PMC6461439 DOI: 10.7554/elife.44556] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
Transient Receptor Potential Melastatin 2 (TRPM2) is a cation channel important for the immune response, insulin secretion, and body temperature regulation. It is activated by cytosolic ADP ribose (ADPR) and contains a nudix-type motif 9 (NUDT9)-homology (NUDT9-H) domain homologous to ADPR phosphohydrolases (ADPRases). Human TRPM2 (hsTRPM2) is catalytically inactive due to mutations in the conserved Nudix box sequence. Here, we show that TRPM2 Nudix motifs are canonical in all invertebrates but vestigial in vertebrates. Correspondingly, TRPM2 of the cnidarian Nematostella vectensis (nvTRPM2) and the choanoflagellate Salpingoeca rosetta (srTRPM2) are active ADPRases. Disruption of ADPRase activity fails to affect nvTRPM2 channel currents, reporting a catalytic cycle uncoupled from gating. Furthermore, pore sequence substitutions responsible for inactivation of hsTRPM2 also appeared in vertebrates. Correspondingly, zebrafish (Danio rerio) TRPM2 (drTRPM2) and hsTRPM2 channels inactivate, but srTRPM2 and nvTRPM2 currents are stable. Thus, catalysis and pore stability were lost simultaneously in vertebrate TRPM2 channels.
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Affiliation(s)
- Iordan Iordanov
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - Balázs Tóth
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - Andras Szollosi
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - László Csanády
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
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11
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Fliegert R, Watt JM, Schöbel A, Rozewitz MD, Moreau C, Kirchberger T, Thomas MP, Sick W, Araujo AC, Harneit A, Potter BVL, Guse AH. Ligand-induced activation of human TRPM2 requires the terminal ribose of ADPR and involves Arg1433 and Tyr1349. Biochem J 2017; 474:2159-2175. [PMID: 28515263 PMCID: PMC5473349 DOI: 10.1042/bcj20170091] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 12/23/2022]
Abstract
TRPM2 (transient receptor potential channel, subfamily melastatin, member 2) is a Ca2+-permeable non-selective cation channel activated by the binding of adenosine 5'-diphosphoribose (ADPR) to its cytoplasmic NUDT9H domain (NUDT9 homology domain). Activation of TRPM2 by ADPR downstream of oxidative stress has been implicated in the pathogenesis of many human diseases, rendering TRPM2 an attractive novel target for pharmacological intervention. However, the structural basis underlying this activation is largely unknown. Since ADP (adenosine 5'-diphosphate) alone did not activate or antagonize the channel, we used a chemical biology approach employing synthetic analogues to focus on the role of the ADPR terminal ribose. All novel ADPR derivatives modified in the terminal ribose, including that with the seemingly minor change of methylating the anomeric-OH, abolished agonist activity at TRPM2. Antagonist activity improved as the terminal substituent increasingly resembled the natural ribose, indicating that gating by ADPR might require specific interactions between hydroxyl groups of the terminal ribose and the NUDT9H domain. By mutating amino acid residues of the NUDT9H domain, predicted by modelling and docking to interact with the terminal ribose, we demonstrate that abrogating hydrogen bonding of the amino acids Arg1433 and Tyr1349 interferes with activation of the channel by ADPR. Taken together, using the complementary experimental approaches of chemical modification of the ligand and site-directed mutagenesis of TRPM2, we demonstrate that channel activation critically depends on hydrogen bonding of Arg1433 and Tyr1349 with the terminal ribose. Our findings allow for a more rational design of novel TRPM2 antagonists that may ultimately lead to compounds of therapeutic potential.
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Affiliation(s)
- Ralf Fliegert
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Joanna M Watt
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Anja Schöbel
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Monika D Rozewitz
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
| | - Tanja Kirchberger
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Mark P Thomas
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
| | - Wiebke Sick
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Andrea C Araujo
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Angelika Harneit
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Barry V L Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, U.K
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Andreas H Guse
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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12
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Valkov E, Jonas S, Weichenrieder O. Mille viae in eukaryotic mRNA decapping. Curr Opin Struct Biol 2017; 47:40-51. [PMID: 28591671 DOI: 10.1016/j.sbi.2017.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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Affiliation(s)
- Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zürich, Otto-Stern Weg 3, 8093 Zürich, Switzerland.
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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13
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Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The evolution of function within the Nudix homology clan. Proteins 2017; 85:775-811. [PMID: 27936487 PMCID: PMC5389931 DOI: 10.1002/prot.25223] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/15/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed a structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775-811. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John R. Srouji
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Present address: Molecular and Cellular Biology DepartmentHarvard UniversityCambridgeMassachusetts02138
| | - Anting Xu
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Annsea Park
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
| | - Jack F. Kirsch
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Steven E. Brenner
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
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14
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Bischler T, Hsieh PK, Resch M, Liu Q, Tan HS, Foley PL, Hartleib A, Sharma CM, Belasco JG. Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets. J Biol Chem 2016; 292:1934-1950. [PMID: 27974459 DOI: 10.1074/jbc.m116.761171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
RNA degradation is crucial for regulating gene expression in all organisms. Like the decapping of eukaryotic mRNAs, the conversion of the 5'-terminal triphosphate of bacterial transcripts to a monophosphate can trigger RNA decay by exposing the transcript to attack by 5'-monophosphate-dependent ribonucleases. In both biological realms, this deprotection step is catalyzed by members of the Nudix hydrolase family. The genome of the gastric pathogen Helicobacter pylori, a Gram-negative epsilonproteobacterium, encodes two proteins resembling Nudix enzymes. Here we present evidence that one of them, HP1228 (renamed HpRppH), is an RNA pyrophosphohydrolase that triggers RNA degradation in H. pylori, whereas the other, HP0507, lacks such activity. In vitro, HpRppH converts RNA 5'-triphosphates and diphosphates to monophosphates. It requires at least two unpaired nucleotides at the 5' end of its substrates and prefers three or more but has only modest sequence preferences. The influence of HpRppH on RNA degradation in vivo was examined by using RNA-seq to search the H. pylori transcriptome for RNAs whose 5'-phosphorylation state and cellular concentration are governed by this enzyme. Analysis of cDNA libraries specific for transcripts bearing a 5'-triphosphate and/or monophosphate revealed at least 63 potential HpRppH targets. These included mRNAs and sRNAs, several of which were validated individually by half-life measurements and quantification of their 5'-terminal phosphorylation state in wild-type and mutant cells. These findings demonstrate an important role for RppH in post-transcriptional gene regulation in pathogenic Epsilonproteobacteria and suggest a possible basis for the phenotypes of H. pylori mutants lacking this enzyme.
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Affiliation(s)
- Thorsten Bischler
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Ping-Kun Hsieh
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Marcus Resch
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Quansheng Liu
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Hock Siew Tan
- the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Patricia L Foley
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Anika Hartleib
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and
| | - Cynthia M Sharma
- From the Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany; the Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, 97080 Würzburg, Germany and.
| | - Joel G Belasco
- the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, New York 10016.
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15
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Singh PK, Shrivastava AK, Singh S, Rai R, Chatterjee A, Rai LC. Alr2954 of Anabaena sp. PCC 7120 with ADP-ribose pyrophosphatase activity bestows abiotic stress tolerance in Escherichia coli. Funct Integr Genomics 2016; 17:39-52. [PMID: 27778111 DOI: 10.1007/s10142-016-0531-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 01/23/2023]
Abstract
In silico derived properties on experimental validation revealed that hypothetical protein Alr2954 of Anabaena sp. PCC7120 is ADP-ribose pyrophosphatase, which belongs to nudix hydrolase superfamily. Presence of ADP-ribose binding site was attested by ADP-ribose pyrophosphatase activity (K m 44.71 ± 8.043 mM, V max 7.128 ± 0.417 μmol min-1 mg protein-1, and K cat/K m 9.438 × 104 μM-1 min-1). Besides ADP-ribose, the enzyme efficiently hydrolyzed various nucleoside phosphatases such as 8-oxo-dGDP, 8-oxo-dADP, 8-oxo-dGTP, 8-oxo-dATP, GDP-mannose, ADP-glucose, and NADH. qRT-PCR analysis of alr2954 showed significant expression under different abiotic stresses reconfirming its role in stress tolerance. Thus, Alr2954 qualifies to be a member of nudix hydrolase superfamily, which serves as ADP-ribose pyrophosphatase and assists in multiple abiotic stress tolerance.
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Affiliation(s)
- Prashant Kumar Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Alok Kumar Shrivastava
- Department of Chemical Engineering, Indian Institute of Technology, Banaras Hindu University, Vranasi, 221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ruchi Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Antra Chatterjee
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - L C Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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16
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Furuike Y, Akita Y, Miyahara I, Kamiya N. ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors. Biochemistry 2016; 55:1801-12. [PMID: 26979298 DOI: 10.1021/acs.biochem.5b00886] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn(2+), Zn(2+), or Mg(2+) as cofactors. Here, we report the reaction pathway observed in the catalytic center of TtADPRase, based on cryo-trapping X-ray crystallography at atomic resolutions around 1.0 Å using Mn(2+) as the reaction trigger, which was soaked into TtADPRase-ADPR binary complex crystals. Integrating 11 structures along the reaction timeline, five reaction states of TtADPRase were assigned, which were ADPRase alone (E), the ADPRase-ADPR binary complex (ES), two ADPRase-ADPR-Mn(2+) reaction intermediates (ESM, ESMM), and the postreaction state (E'). Two Mn(2+) ions were inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states. The ADPR-hydrolysis reaction was characterized by electrostatic, proximity, and orientation effects, and by preferential binding for the transition state. A new reaction mechanism is proposed, which differs from previous ones suggested from structure analyses with nonhydrolyzable substrate analogues or point-mutated ADPRases.
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Affiliation(s)
- Yoshihiko Furuike
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Yuka Akita
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Ikuko Miyahara
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Nobuo Kamiya
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
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17
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Daniels CM, Thirawatananond P, Ong SE, Gabelli SB, Leung AKL. Nudix hydrolases degrade protein-conjugated ADP-ribose. Sci Rep 2015; 5:18271. [PMID: 26669448 PMCID: PMC4680915 DOI: 10.1038/srep18271] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/03/2015] [Indexed: 12/25/2022] Open
Abstract
ADP-ribosylation refers to the transfer of the ADP-ribose group from NAD(+) to target proteins post-translationally, either attached singly as mono(ADP-ribose) (MAR) or in polymeric chains as poly(ADP-ribose) (PAR). Though ADP-ribosylation is therapeutically important, investigation of this protein modification has been limited by a lack of proteomic tools for site identification. Recent work has demonstrated the potential of a tag-based pipeline in which MAR/PAR is hydrolyzed down to phosphoribose, leaving a 212 Dalton tag at the modification site. While the pipeline has been proven effective by multiple groups, a barrier to application has become evident: the enzyme used to transform MAR/PAR into phosphoribose must be purified from the rattlesnake Crotalus adamanteus venom, which is contaminated with proteases detrimental for proteomic applications. Here, we outline the steps necessary to purify snake venom phosphodiesterase I (SVP) and describe two alternatives to SVP-the bacterial Nudix hydrolase EcRppH and human HsNudT16. Importantly, expression and purification schemes for these Nudix enzymes have already been proven, with high-quality yields easily attainable. We demonstrate their utility in identifying ADP-ribosylation sites on Poly(ADP-ribose) Polymerase 1 (PARP1) with mass spectrometry and discuss a structure-based rationale for this Nudix subclass in degrading protein-conjugated ADP-ribose, including both MAR and PAR.
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Affiliation(s)
- Casey M. Daniels
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Puchong Thirawatananond
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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18
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de la Peña AH, Suarez A, Duong-ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One 2015; 10:e0141716. [PMID: 26524597 PMCID: PMC4629899 DOI: 10.1371/journal.pone.0141716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.
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Affiliation(s)
- Andres H. de la Peña
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Allison Suarez
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Krisna C. Duong-ly
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew J. Schoeffield
- Biology Department, Loyola University Maryland, Baltimore, Maryland, United States of America
| | - Mario A. Pizarro-Dupuy
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melissa Zarr
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Silvia A. Pineiro
- Department of Medical and Research Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - L. Mario Amzel
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sandra B. Gabelli
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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19
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Abstract
Universal and ubiquitous redox cofactors, nicotinamide adenine dinucleotide (NAD) and its phosphorylated analog (NADP), collectively contribute to approximately 12% of all biochemical reactions included in the metabolic model of Escherichia coli K-12. A homeostasis of the NAD pool faithfully maintained by the cells results from a dynamic balance in a network of NAD biosynthesis, utilization, decomposition, and recycling pathways that is subject to tight regulation at various levels. A brief overview of NAD utilization processes is provided in this review, including some examples of nonredox utilization. The review focuses mostly on those aspects of NAD biogenesis and utilization in E. coli and Salmonella that emerged within the past 12 years. The first pyridine nucleotide cycle (PNC) originally identified in mammalian systems and termed the Preiss-Handler pathway includes a single-step conversion of niacin (Na) to NaMN by nicotinic acid phosphoribosyltransferase (PncB). In E. coli and many other prokaryotes, this enzyme, together with nicotinamide deamidase (PncA), compose the major pathway for utilization of the pyridine ring in the form of amidated (Nm) or deamidated (Na) precursors. The existence of various regulatory mechanisms and checkpoints that control the NAD biosynthetic machinery reflects the importance of maintaining NAD homeostasis in a variety of growth conditions. Among the most important regulatory mechanisms at the level of individual enzymes are a classic feedback inhibition of NadB, the first enzyme of NAD de novo biosynthesis, by NAD and a metabolic regulation of NadK by reduced cofactors.
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20
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Vasilyev N, Serganov A. Structures of RNA complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5'-end-dependent mRNA decay. J Biol Chem 2015; 290:9487-99. [PMID: 25657011 DOI: 10.1074/jbc.m114.634824] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Indexed: 12/20/2022] Open
Abstract
5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-π contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria.
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Affiliation(s)
- Nikita Vasilyev
- From the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016
| | - Alexander Serganov
- From the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016
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21
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Modzelan M, Kujawa M, Głąbski K, Jagura-Burdzy G, Kraszewska E. NudC Nudix hydrolase from Pseudomonas syringae, but not its counterpart from Pseudomonas aeruginosa, is a novel regulator of intracellular redox balance required for growth, motility and biofilm formation. Mol Microbiol 2014; 93:867-82. [PMID: 24989777 DOI: 10.1111/mmi.12702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2014] [Indexed: 11/29/2022]
Abstract
Nudix pyrophosphatases, ubiquitous in all organisms, have not been well studied. Recent implications that some of them may be involved in response to stress and in pathogenesis indicate that they play important biological functions. We have investigated NudC Nudix proteins from the plant pathogen Pseudomonas syringae pv. tomato str. DC3000 and from the human pathogen Pseudomonas aeruginosa PAO1161. We found that these homologous enzymes are homodimeric and in vitro preferentially hydrolyse NADH. The P. syringae mutant strain deficient in NudC accumulated NADH and displayed significant defects in growth, motility and biofilm formation. The wild type copy of the nudC gene with its cognate promoter delivered in trans into the nudC mutant restored its fitness. However, introduction of the P. syringae nudC gene under the control of the strong tacp promoter into either P. syringae or P. aeruginosa cells had a toxic effect on both strains. Opposite to P. syringae NudC, the P. aeruginosa NudC deficiency as well as its overproduction had no visible impact on cells. Moreover, P. aeruginosa NudC does not compensate the lack of its counterpart in the P. syringae mutant. These results indicate that NudC from P. syringae, but not from P. aeruginosa is vital for bacteria.
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Affiliation(s)
- Marta Modzelan
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
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22
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Hong MK, Ribeiro AJM, Kim JK, Ngo HPT, Kim J, Lee CH, Ahn YJ, Fernandes PA, Li Q, Ramos MJ, Kang LW. Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli. ACTA ACUST UNITED AC 2014; 70:1297-310. [PMID: 24816099 DOI: 10.1107/s1399004714002570] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/04/2014] [Indexed: 11/10/2022]
Abstract
YmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner. The structures of YmfB alone and in complex with three sulfates and two manganese ions determined by X-ray crystallography, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB. Mass-spectrometric analysis confirmed that water attacks the terminal phosphates of GTP and GDP sequentially. Kinetic analysis of binding-site mutants showed that no individual residue is absolutely required for catalytic activity, suggesting that protein residues do not participate in the deprotonation of the attacking water. Thermodynamic integration calculations show that a hydroxyl ion bound to two divalent metal ions attacks the phosphate directly without the help of a nearby catalytic base.
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Affiliation(s)
- Myoung-Ki Hong
- Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - António J M Ribeiro
- Requimte/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Jin-Kwang Kim
- Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Jiyoung Kim
- Department of Bioscience and Biotechnology and Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology and Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Yeh-Jin Ahn
- Department of Green Life Science, College of Convergence, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea
| | - Pedro Alexandrino Fernandes
- Requimte/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Qing Li
- School of Pharmaceutical Sciences, Center for Cellular and Structural Biology, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Maria Joao Ramos
- Requimte/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, 1 Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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23
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Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure 2013; 21:1571-80. [PMID: 23911090 DOI: 10.1016/j.str.2013.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/16/2022]
Abstract
Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.
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Affiliation(s)
- Robin A Aglietti
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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24
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Piton J, Larue V, Thillier Y, Dorléans A, Pellegrini O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisné C, Condon C. Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proc Natl Acad Sci U S A 2013; 110:8858-63. [PMID: 23610407 PMCID: PMC3670357 DOI: 10.1073/pnas.1221510110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. Here we present the crystal structures of Bacillus subtilis RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to Bdellovibrio bacteriovorus RppH, which recognizes the first nucleotide of its RNA targets, the B. subtilis enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.
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Affiliation(s)
- Jérémie Piton
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Valéry Larue
- Unité Mixte de Recherche (UMR) 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; and
| | - Yann Thillier
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Audrey Dorléans
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Olivier Pellegrini
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Inés Li de la Sierra-Gallay
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS–Université Montpellier 1–Université Montpellier 2, 34095 Montpellier Cedex 05, France
| | - Carine Tisné
- Unité Mixte de Recherche (UMR) 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; and
| | - Ciarán Condon
- Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité) Institut de Biologie Physico-Chimique, 75005 Paris, France
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25
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Boto AN, Xu W, Jakoncic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, Amzel LM. Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition. Proteins 2011; 79:2455-66. [PMID: 21638333 PMCID: PMC3164844 DOI: 10.1002/prot.23069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/05/2011] [Accepted: 04/19/2011] [Indexed: 01/02/2023]
Abstract
The Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX(5)EX(7)REUXEEXGU (where U is I, L, or V), is a well-studied family in which relations have been established between primary sequence and substrate specificity for many members. For example, enzymes that hydrolyze the diphosphate linkage of ADP-ribose are characterized by having a proline 15 amino acids C-terminal of the Nudix signature sequence. GDPMK is a Nudix enzyme that conserves this characteristic proline but uses GDP-mannose as the preferred substrate. By investigating the structure of the GDPMK alone, bound to magnesium, and bound to substrate, the structural basis for this divergent substrate specificity and a new rule was identified by which ADP-ribose pyrophosphatases can be distinguished from purine-DP-mannose pyrophosphatases from primary sequence alone. Kinetic and mutagenesis studies showed that GDPMK hydrolysis does not rely on a single glutamate as the catalytic base. Instead, catalysis is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. GDPMK was thought to play a role in biofilm formation because of its upregulation in response to RcsC signaling; however, GDPMK knockout strains show no defect in their capacity of forming biofilms.
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Affiliation(s)
- Agedi N. Boto
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Wenlian Xu
- Department of Biology. School of Arts and Sciences. Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jean Jakoncic
- Brookhaven National Laboratory, National Synchrotron Light Source, Building 725, Upton, NY 11973, USA
| | - Archana Pannuri
- Department of Microbiology and Cell Science. University of Florida. Gainesville, FL 32611-0700, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science. University of Florida. Gainesville, FL 32611-0700, USA
| | - Maurice J. Bessman
- Department of Biology. School of Arts and Sciences. Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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26
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Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y. Diverse substrate recognition and hydrolysis mechanisms of human NUDT5. Nucleic Acids Res 2011; 39:8972-83. [PMID: 21768126 PMCID: PMC3203587 DOI: 10.1093/nar/gkr575] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Human NUDT5 (hNUDT5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dGDP, 8-oxo-dADP and ADP-ribose (ADPR). However, the structural basis of the broad substrate specificity remains unknown. Here, we report the crystal structures of hNUDT5 complexed with 8-oxo-dGDP and 8-oxo-dADP. These structures reveal an unusually different substrate-binding mode. In particular, the positions of two phosphates (α and β phosphates) of substrate in the 8-oxo-dGDP and 8-oxo-dADP complexes are completely inverted compared with those in the previously reported hNUDT5–ADPR complex structure. This result suggests that the nucleophilic substitution sites of the substrates involved in hydrolysis reactions differ despite the similarities in the chemical structures of the substrates and products. To clarify this hypothesis, we employed the isotope-labeling method and revealed that 8-oxo-dGDP is attacked by nucleophilic water at Pβ, whereas ADPR is attacked at Pα. This observation reveals that the broad substrate specificity of hNUDT5 is achieved by a diversity of not only substrate recognition, but also hydrolysis mechanisms and leads to a novel aspect that enzymes do not always catalyze the reaction of substrates with similar chemical structures by using the chemically equivalent reaction site.
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Affiliation(s)
- Takao Arimori
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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27
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Duong-Ly KC, Gabelli SB, Xu W, Dunn CA, Schoeffield AJ, Bessman MJ, Amzel LM. The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities. J Bacteriol 2011; 193:3175-85. [PMID: 21531795 PMCID: PMC3133267 DOI: 10.1128/jb.00089-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 04/22/2011] [Indexed: 11/20/2022] Open
Abstract
A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'→5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-Å resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
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Affiliation(s)
- Krisna C. Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - WenLian Xu
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | - Christopher A. Dunn
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | | | - Maurice J. Bessman
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland 21218
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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28
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Tong L, Denu JM. Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1617-25. [PMID: 20176146 PMCID: PMC3310390 DOI: 10.1016/j.bbapap.2010.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 02/04/2010] [Accepted: 02/07/2010] [Indexed: 10/19/2022]
Abstract
Sirtuins catalyze the NAD(+)-dependent deacetylation of target proteins, which are regulated by this reversible lysine modification. During deacetylation, the glycosidic bond of the nicotinamide ribose is cleaved to yield nicotinamide and the ribose accepts the acetyl group from substrate to produce O-acetyl-ADP-ribose (OAADPr), which exists as an approximately 50:50 mixture of 2' and 3' isomers at neutral pH. Discovery of this metabolite has fueled the idea that OAADPr may play an important role in the biology associated with sirtuins, acting as a signaling molecule and/or an important substrate for downstream enzymatic processes. Evidence for OAADPr-metabolizing enzymes indicates that at least three distinct activities exist that could modulate the cellular levels of this NAD(+)-derived metabolite. In Saccharomyces cerevisiae, NUDIX hydrolase Ysa1 cleaves OAADPr to AMP and 2- and 3-O-acetylribose-5-phosphate, lowering the cellular levels of OAADPr. A buildup of OAADPr and ADPr has been linked to a metabolic shift that lowers endogenous reactive oxygen species and diverts glucose towards preventing oxidative damage. In vitro, the mammalian enzyme ARH3 hydrolyzes OAADPr to acetate and ADPr. A third nuclear-localized activity appears to utilize OAADPr to transfer the acetyl-group to another small molecule, whose identity remains unknown. Recent studies suggest that OAADPr may regulate gene silencing by facilitating the assembly and loading of the Sir2-4 silencing complex onto nucleosomes. In mammalian cells, the Trpm2 cation channel is gated by both OAADPr and ADP-ribose. Binding is mediated by the NUDIX homology (NudT9H) domain found within the intracellular portion of the channel. OAADPr is capable of binding the Macro domain of splice variants from histone protein MacroH2A, which is highly enriched at heterochromatic regions. With recently developed tools, the pace of new discoveries of OAADPr-dependent processes should facilitate new molecular insight into the diverse biological processes modulated by sirtuins.
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Affiliation(s)
- Lei Tong
- Department of Biomolecular Chemistry, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, 53706
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, 53706
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29
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Joye IJ, Beliën T, Delcour JA. The first characterised wheat (Triticum aestivum L.) member of the nudix hydrolase family shows specificity for NAD(P)(H) and FAD. J Cereal Sci 2010. [DOI: 10.1016/j.jcs.2010.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Nakamura T, Meshitsuka S, Kitagawa S, Abe N, Yamada J, Ishino T, Nakano H, Tsuzuki T, Doi T, Kobayashi Y, Fujii S, Sekiguchi M, Yamagata Y. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. J Biol Chem 2010; 285:444-52. [PMID: 19864691 PMCID: PMC2804192 DOI: 10.1074/jbc.m109.066373] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/14/2009] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in DNA. Of the several enzymes that recognize 8-oxoguanine, MutT exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. The crystal structures of MutT in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dGMP and 8-oxo-dGMP plus Mn(2+), respectively, were determined. MutT strictly recognizes the overall conformation of 8-oxo-dGMP through a number of hydrogen bonds. This recognition mode revealed that 8-oxoguanine nucleotides are discriminated from guanine nucleotides by not only the hydrogen bond between the N7-H and Odelta (N119) atoms but also by the syn glycosidic conformation that 8-oxoguanine nucleotides prefer. Nevertheless, these discrimination factors cannot by themselves explain the roughly 34,000-fold difference between the affinity of MutT for 8-oxo-dGMP and dGMP. When the binary complex of MutT with 8-oxo-dGMP is compared with the ligand-free form, ordering and considerable movement of the flexible loops surrounding 8-oxo-dGMP in the binary complex are observed. These results indicate that MutT specifically recognizes 8-oxoguanine nucleotides by the ligand-induced conformational change.
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Affiliation(s)
- Teruya Nakamura
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Sachiko Meshitsuka
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Seiju Kitagawa
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Nanase Abe
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Junichi Yamada
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Tetsuya Ishino
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Hiroaki Nakano
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Teruhisa Tsuzuki
- the Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582
| | - Takefumi Doi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Yuji Kobayashi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Satoshi Fujii
- the School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, and
| | | | - Yuriko Yamagata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
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31
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Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure 2009; 17:939-51. [PMID: 19604474 DOI: 10.1016/j.str.2009.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 04/21/2009] [Accepted: 05/06/2009] [Indexed: 01/12/2023]
Abstract
Besides its function as an essential redox cofactor, nicotinamide adenine dinucleotide (NAD) also serves as a consumable substrate for several reactions with broad impact on many cellular processes. NAD homeostasis appears to be tightly controlled, but the mechanism of its regulation is little understood. Here we demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses the transcription of NAD biosynthetic genes in vitro. The NAD metabolite ADP-ribose functions as an activator suppressing NrtR repressor activity. The presence of high ADP-ribose levels in the cell is indicative of active NAD turnover in bacteria, which could signal the activation of NAD biosynthetic gene expression via inhibiting the repressor function of NrtR. By comparing the crystal structures of NrtR in complex with DNA and with ADP-ribose, we identified a "Nudix switch" element that likely plays a critical role in the allosteric regulation of DNA binding and repressor function of NrtR.
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Affiliation(s)
- Nian Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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32
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Thorsell AG, Persson C, Gräslund S, Hammarström M, Busam RD, Hallberg BM. Crystal structure of human diphosphoinositol phosphatase 1. Proteins 2009; 77:242-6. [DOI: 10.1002/prot.22489] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Structure 2009; 17:472-81. [PMID: 19278661 DOI: 10.1016/j.str.2008.12.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 12/08/2008] [Accepted: 12/29/2008] [Indexed: 11/22/2022]
Abstract
Until recently, the mechanism of mRNA decay in bacteria was thought to be different from that of eukaryotes. This paradigm changed with the discovery that RppH (ORF176/NudH/YgdP), an Escherichia coli enzyme that belongs to the Nudix superfamily, is an RNA pyrophosphohydrolase that initiates mRNA decay by cleaving pyrophosphate from the 5'-triphosphate. Here we report the 1.9 Angstroms resolution structure of the Nudix hydrolase BdRppH from Bdellovibrio bacteriovorus, a bacterium that feeds on other Gram-negative bacteria. Based on the structure of the enzyme alone and in complex with GTP-Mg2+, we propose a mode of RNA binding similar to that of the nuclear decapping enzyme from Xenopus laevis, X29. In additional experiments, we show that BdRppH can indeed function in vitro and in vivo as an RNA pyrophosphohydrolase. These findings set the basis for the identification of possible decapping enzymes in other bacteria.
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34
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Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem J 2009; 420:27-35. [PMID: 19210265 DOI: 10.1042/bj20082296] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Decapping enzymes are required for the removal of the 5'-end cap of mRNAs. These enzymes exhibit a specific hydrolase activity, resulting in cleavage between the alpha- and beta-phosphates of the m7GpppN cap to generate both m7GDP and monophosphorylated RNA products. Decapping enzymes have been found in humans, plants and yeasts, and have been discovered more recently in vaccinia virus (D10 protein). Although experimental evidences are lacking, three-metal- and two-metal-ion mechanisms have been proposed so far for the decapping enzymes. In the present study, we performed a biochemical characterization of the interaction of bivalent cations with the vaccinia virus D10 protein. Synergistic activation of the enzyme was observed in the presence of Mg2+ and Mn2+ ions, suggesting the existence of two metal-ion-binding sites on the D10 protein. Moreover, dual-ligand titration experiments using fluorescence spectroscopy demonstrated the presence of two metal-ion-binding sites on the enzyme. A three-dimensional structural model of the active site of the enzyme was generated which highlighted the importance of three glutamate residues involved in the co-ordination of two metal ions and a water molecule. Mutational analyses confirmed the role of two glutamate residues for the binding of metal ions. We demonstrate that one metal ion is co-ordinated by Glu132, while the second metal ion is co-ordinated by Glu145. Taken together, these results support the proposed two-metal-ion mechanistic model for the D10 decapping enzyme.
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35
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Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009; 5:e1000362. [PMID: 19197347 PMCID: PMC2628731 DOI: 10.1371/journal.pgen.1000362] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/31/2008] [Indexed: 11/19/2022] Open
Abstract
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
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36
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Trésaugues L, Stenmark P, Schüler H, Flodin S, Welin M, Nyman T, Hammarström M, Moche M, Gräslund S, Nordlund P. The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site. Proteins 2008; 73:1047-52. [PMID: 18767156 DOI: 10.1002/prot.22198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lionel Trésaugues
- Department of Medical Biochemistry and Biophysics, Structural Genomics Consortium, Karolinska Institute, Stockholm, Sweden
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Binkowski TA, Joachimiak A. Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites. BMC STRUCTURAL BIOLOGY 2008; 8:45. [PMID: 18954462 PMCID: PMC2626596 DOI: 10.1186/1472-6807-8-45] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/27/2008] [Indexed: 12/02/2022]
Abstract
Background Protein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role. Results We describe a methodology that attempts to optimize two components, global shape and local physicochemical texture, for evaluating the similarity between a pair of surfaces. Surface shape similarity is assessed using a three-dimensional object recognition algorithm and physicochemical texture similarity is assessed through a spatial alignment of conserved residues between the surfaces. The comparisons are used in tandem to efficiently search the Global Protein Surface Survey (GPSS), a library of annotated surfaces derived from structures in the PDB, for studying evolutionary relationships and uncovering novel similarities between proteins. Conclusion We provide an assessment of our method using library retrieval experiments for identifying functionally homologous surfaces binding different ligands, functionally diverse surfaces binding the same ligand, and binding surfaces of ubiquitous and conformationally flexible ligands. Results using surface similarity to predict function for proteins of unknown function are reported. Additionally, an automated analysis of the ATP binding surface landscape is presented to provide insight into the correlation between surface similarity and function for structures in the PDB and for the subset of protein kinases.
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Affiliation(s)
- T Andrew Binkowski
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
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38
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Floor SN, Jones BN, Gross JD. Control of mRNA decapping by Dcp2: An open and shut case? RNA Biol 2008; 5:189-92. [PMID: 18971632 DOI: 10.4161/rna.6859] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
mRNA decapping by Dcp2 is a critical step in several major eukaryotic mRNA decay pathways. Dcp2 forms the catalytic core of a mRNP that is configured for processing diverse substrates by pathway-specific activators. Here we elaborate a model of catalysis by Dcp2 which posits that activity is controlled by a conformational equilibrium between an open, inactive and closed, active form of the enzyme. Structural studies on yeast Dcp2 indicate that the general activator Dcp1 and substrate promote the closed form of the enzyme. Kinetic studies indicate the catalytic step of decapping is rate-limiting and accelerated by Dcp1. We propose that regulation of conformational transitions in Dcp2 during a rate-limiting step after assembly of the decapping mRNP provides a checkpoint for determining if an mRNA is degraded or recycled to translation.
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Affiliation(s)
- Stephen N Floor
- Graduate Group in Biophysics, University of California, San Francisco, California 94158-2517, USA
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Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H. Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure 2008; 16:196-209. [PMID: 18275811 DOI: 10.1016/j.str.2007.11.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 10/30/2007] [Accepted: 11/18/2007] [Indexed: 11/28/2022]
Abstract
Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.
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Affiliation(s)
- Nian Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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40
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Zha M, Guo Q, Zhang Y, Yu B, Ou Y, Zhong C, Ding J. Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies. J Mol Biol 2008; 379:568-78. [PMID: 18462755 DOI: 10.1016/j.jmb.2008.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 03/31/2008] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
Abstract
Human NUDT5 (hNUDT5) is an ADP-ribose (ADPR) pyrophosphatase (ADPRase) that plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5'-phosphate. We report the crystal structure of hNUDT5 in complex with a non-hydrolyzable ADPR analogue, alpha,beta-methyleneadenosine diphosphoribose, and three Mg(2+) ions representing the transition state of the enzyme during catalysis. Analysis of this structure and comparison with previously reported hNUDT5 structures identify key residues involved in substrate binding and catalysis. In the transition-state structure, three metal ions are bound at the active site and are coordinated by surrounding residues and water molecules. A conserved water molecule is at an ideal position for nucleophilic attack on the alpha-phosphate of ADPR. The side chain of Glu166 on loop L9 changes its conformation to interact with the conserved water molecule compared with that in the substrate-bound structure and appears to function as a catalytic base. Mutagenesis and kinetic studies show that Trp28 and Trp46 are important for the substrate binding; Arg51 is involved in both the substrate binding and the catalysis; and Glu112 and Glu116 of the Nudix motif, Glu166 on loop L9, and Arg111 are critical for the catalysis. The structural and biochemical data together reveal the molecular basis of the catalytic mechanism of ADPR hydrolysis by hNUDT5. Specifically, Glu166 functions as a catalytic base to deprotonate a conserved water molecule that acts as a nucleophile to attack the alpha-phosphate of ADPR, and three Mg(2+) ions are involved in the activation of the nucleophile and the binding of the substrate. Structural comparison of different ADPRases also suggests that most dimeric ADPRases may share a similar catalytic mechanism of ADPR hydrolysis.
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Affiliation(s)
- Manwu Zha
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
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41
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Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross JD. mRNA decapping is promoted by an RNA-binding channel in Dcp2. Mol Cell 2008; 29:324-36. [PMID: 18280238 DOI: 10.1016/j.molcel.2007.11.027] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/26/2007] [Accepted: 11/26/2007] [Indexed: 11/25/2022]
Abstract
Cap hydrolysis by Dcp2 is a critical step in several eukaryotic mRNA decay pathways. Processing requires access to cap-proximal nucleotides and the coordinated assembly of a decapping mRNP, but the mechanism of substrate recognition and regulation by protein interactions have remained elusive. Using NMR spectroscopy and kinetic analyses, we show that yeast Dcp2 resolves interactions with the cap and RNA body using a bipartite surface that forms a channel intersecting the catalytic and regulatory Dcp1-binding domains. The interaction with cap is weak but specific and requires binding of the RNA body to a dynamic interface. The catalytic step is stimulated by Dcp1 and its interaction domain, likely through a substrate-induced conformational change. Thus, activation of the decapping mRNP is restricted by access to 5'-proximal nucleotides, a feature that could act as a checkpoint in mRNA metabolism.
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Affiliation(s)
- Mandar V Deshmukh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94107, USA
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42
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Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R. Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8. J Bacteriol 2008; 190:1108-17. [PMID: 18039767 PMCID: PMC2223557 DOI: 10.1128/jb.01522-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 11/12/2007] [Indexed: 11/20/2022] Open
Abstract
ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.
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Affiliation(s)
- Taisuke Wakamatsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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43
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Peculis BA, Reynolds K, Cleland M. Metal Determines Efficiency and Substrate Specificity of the Nuclear NUDIX Decapping Proteins X29 and H29K (Nudt16). J Biol Chem 2007; 282:24792-805. [PMID: 17567574 DOI: 10.1074/jbc.m704179200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Xenopus X29 protein was identified by its high affinity binding to U8 small nucleolar RNA, a small nucleolar RNA required for ribosome biogenesis. X29 and its human homologue H29K (Nudt16) are nuclear nucleoside diphosphatase proteins localized within foci in the nucleolus and nucleoplasm. These proteins can remove m(7)G and m(227)G caps from RNAs, rendering them substrates for 5'-3' exonucleases for degradation in vivo. Here, a more complete characterization of these metal-dependent decapping proteins demonstrates that the metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg(+2) the proteins hydrolyze the 5' cap from only one RNA substrate: U8 small nucleolar RNA. However, in the presence of Mn(+2) or Co(+2) all RNAs are substrates and the decapping efficiency is higher. The x-ray crystal structure of X29 facilitated structure-based mutagenesis. Mutation of single amino acids coordinating metal in the active site yielded mutant proteins confirming essential residues. In vitro assays with purified components are consistent with a lack of protein turnover, apparently due to an inability of the protein to release the decapped RNA, implicating critical in vivo interacting factors. Collectively, these studies indicate that the metal that binds the X29/H29K proteins in vivo may determine whether these decapping proteins function solely as a negative regulator of ribosome biogenesis or can decap a wider variety of nuclear-limited RNAs. With the potential broader RNA substrate specificity, X29/H29K may be the nuclear counterparts of the cytoplasmic decapping machinery, localized in specialized bodies involved in RNA decay.
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Affiliation(s)
- Brenda A Peculis
- Department of Biochemistry, University of Missouri--Columbia, Columbia, Missouri 65211, USA.
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44
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Morán-Zorzano MT, Viale AM, Muñoz FJ, Alonso-Casajús N, Eydallín GG, Zugasti B, Baroja-Fernández E, Pozueta-Romero J. Escherichia coli AspP activity is enhanced by macromolecular crowding and by both glucose-1,6-bisphosphate and nucleotide-sugars. FEBS Lett 2007; 581:1035-40. [PMID: 17306798 DOI: 10.1016/j.febslet.2007.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 01/24/2007] [Accepted: 02/01/2007] [Indexed: 11/25/2022]
Abstract
Escherichia coli ADP-sugar pyrophosphatase (AspP) is a "Nudix" hydrolase that catalyzes the hydrolytic breakdown of ADP-glucose linked to glycogen biosynthesis. Moderate increases of AspP activity in the cell are accompanied by significant reductions of the glycogen content. In vitro analyses showed that AspP activity is strongly enhanced by macromolecular crowding and by both glucose-1,6-bisphosphate and nucleotide-sugars, providing a first set of indicative evidences that AspP is a highly regulated enzyme. To our knowledge, AspP is the sole bacterial enzyme described to date which is activated by both G1,6P(2) and nucleotide-sugars.
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Affiliation(s)
- María Teresa Morán-Zorzano
- Instituto de Agrobiotecnología, Universidad Pública de Navarra/Gobierno de Navarra/Consejo Superior de Investigaciones Científicas, Carretera de Mutilva s/n, 31192 Mutilva Baja, Navarra, Spain
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45
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Zha M, Zhong C, Peng Y, Hu H, Ding J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J Mol Biol 2006; 364:1021-33. [PMID: 17052728 DOI: 10.1016/j.jmb.2006.09.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 09/27/2006] [Accepted: 09/27/2006] [Indexed: 11/23/2022]
Abstract
Human NUDT5 (hNUDT5) is an ADP-ribose pyrophosphatase (ADPRase) belonging to the Nudix hydrolase superfamily. It presumably plays important roles in controlling the intracellular level of ADP-ribose (ADPR) to prevent non-enzymatic ADP-ribosylation by hydrolyzing ADPR to AMP and ribose 5'-phosphate. We report here the crystal structures of hNUDT5 in apo form, in complex with ADPR, and in complex with AMP with bound Mg2+. hNUDT5 forms a homodimer with substantial domain swapping and assumes a structure more similar to Escherichia coli ADPRase ORF209 than human ADPRase NUDT9. The adenine moiety of the substrates is specifically recognized by the enzyme via hydrogen-bonding interactions between N1 and N6 of the base and Glu47 of one subunit, and between N7 of the base and Arg51 of the other subunit, providing the molecular basis for the high selectivity of hNUDT5 for ADP-sugars over other sugar nucleotides. Structural comparisons with E. coli ADPRase ORF209 and ADPXase ORF186 indicate that the existence of an aromatic residue on loop L8 in ORF186 seems to be positively correlated with its enzymatic activity on APnA, whereas hNUDT5 and ORF209 contain no such residue and thus have low or no activities on APnA.
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Affiliation(s)
- Manwu Zha
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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46
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Abstract
[structure: see text] The synthesis of the bisphosphonate ADP-ribose, in which acetylene has replaced the oxygen of the pyrophosphate linkage, is reported.
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Affiliation(s)
- Kim Van derpoorten
- School of Chemistry, David Keir Building, Queen's University Belfast, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland
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47
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Okuda K, Hayashi H, Nishiyama Y. Systematic characterization of the ADP-ribose pyrophosphatase family in the Cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2005; 187:4984-91. [PMID: 15995214 PMCID: PMC1169527 DOI: 10.1128/jb.187.14.4984-4991.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have characterized four putative ADP-ribose pyrophosphatases Sll1054, Slr0920, Slr1134, and Slr1690 in the cyanobacterium Synechocystis sp. strain PCC 6803. Each of the recombinant proteins was overexpressed in Escherichia coli and purified. Sll1054 and Slr0920 hydrolyzed ADP-ribose specifically, while Slr1134 hydrolyzed not only ADP-ribose but also NADH and flavin adenine dinucleotide. By contrast, Slr1690 showed very low activity for ADP-ribose and had four substitutions of amino acids in the Nudix motif, indicating that Slr1690 is not an active ADP-ribose pyrophosphatase. However, the quadruple mutation of Slr1690, T73G/I88E/K92E/A94G, which replaced the mutated amino acids with those conserved in the Nudix motif, resulted in a significant (6.1 x 10(2)-fold) increase in the k(cat) value. These results suggest that Slr1690 might have evolved from an active ADP-ribose pyrophosphatase. Functional and clustering analyses suggested that Sll1054 is a bacterial type, while the other three and Slr0787, which was characterized previously (Raffaelli et al., FEBS Lett. 444:222-226, 1999), are phylogenetically diverse types that originated from an archaeal Nudix protein via molecular evolutionary mechanisms, such as domain fusion and amino acid substitution.
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Affiliation(s)
- Kenji Okuda
- Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Japan
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Kumaran D, Eswaramoorthy S, Studier FW, Swaminathan S. Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme. Protein Sci 2005; 14:719-26. [PMID: 15722447 PMCID: PMC2279289 DOI: 10.1110/ps.041132005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Appr-1''-pase, an important and ubiquitous cellular processing enzyme involved in the tRNA splicing pathway, catalyzes the conversion of ADP-ribose-1''monophosphate (Appr-1''-p) to ADP-ribose. The structures of the native enzyme from the yeast and its complex with ADP-ribose were determined to 1.9 A and 2.05 A, respectively. Analysis of the three-dimensional structure of this protein, selected as a target in a structural genomics project, reveals its putative function and provides clues to the catalytic mechanism. The structure of the 284-amino acid protein shows a two-domain architecture consisting of a three-layer alphabetaalpha sandwich N-terminal domain connected to a small C-terminal helical domain. The structure of Appr-1''-pase in complex with the product, ADP-ribose, reveals an active-site water molecule poised for nucleophilic attack on the terminal phosphate group. Loop-region residues Asn 80, Asp 90, and His 145 may form a catalytic triad.
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Affiliation(s)
- Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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49
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Mildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang LW, Amzel LM. Structures and mechanisms of Nudix hydrolases. Arch Biochem Biophys 2005; 433:129-43. [PMID: 15581572 DOI: 10.1016/j.abb.2004.08.017] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 08/16/2004] [Indexed: 12/12/2022]
Abstract
Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates linked to other moieties, X, and contain the sequence motif or Nudix box, GX(5)EX(7)REUXEEXGU. The mechanisms of Nudix hydrolases are highly diverse in the position on the substrate at which nucleophilic substitution occurs, and in the number of required divalent cations. While most proceed by associative nucleophilic substitutions by water at specific internal phosphorus atoms of a diphosphate or polyphosphate chain, members of the GDP-mannose hydrolase sub-family catalyze dissociative nucleophilic substitutions, by water, at carbon. The site of substitution is likely determined by the positions of the general base and the entering water. The rate accelerations or catalytic powers of Nudix hydrolases range from 10(9)- to 10(12)-fold. The reactions are accelerated 10(3)-10(5)-fold by general base catalysis by a glutamate residue within, or beyond the Nudix box, or by a histidine beyond the Nudix box. Lewis acid catalysis, which contributes 10(3)-10(5)-fold to the rate acceleration, is provided by one, two, or three divalent cations. One divalent cation is coordinated by two or three conserved residues of the Nudix box, the initial glycine and one or two glutamate residues, together with a remote glutamate or glutamine ligand from beyond the Nudix box. Some Nudix enzymes require one (MutT) or two additional divalent cations (Ap(4)AP), to neutralize the charge of the polyphosphate chain, to help orient the attacking hydroxide or oxide nucleophile, and/or to facilitate the departure of the anionic leaving group. Additional catalysis (10-10(3)-fold) is provided by the cationic side chains of lysine and arginine residues and by H-bond donation by tyrosine residues, to orient the general base, or to promote the departure of the leaving group. The overall rate accelerations can be explained by both independent and cooperative effects of these catalytic components.
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Affiliation(s)
- A S Mildvan
- Department of Biological Chemistry, The Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205-2185, USA.
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50
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Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM. Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure 2004; 12:927-35. [PMID: 15274914 DOI: 10.1016/j.str.2004.03.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 03/11/2004] [Accepted: 03/12/2004] [Indexed: 11/18/2022]
Abstract
GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 A X-ray structure of the GDPMH-Mg(2+)-GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction. Several residues and the divalent cation strongly promote the departure of the GDP leaving group, supporting a dissociative mechanism. Comparison of the GDPMH structure with that of a typical Nudix hydrolase suggests how sequence changes result in the switch of catalytic activity from P-O bond cleavage to C-O bond cleavage. Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A.
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Affiliation(s)
- Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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