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Busby JN, Trevelyan S, Pegg CL, Kerr ED, Schulz BL, Chassagnon I, Landsberg MJ, Weston MK, Hurst MRH, Lott JS. The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo. IUCrJ 2024; 11:299-308. [PMID: 38512773 PMCID: PMC11067744 DOI: 10.1107/s2052252524001969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB-TcC subcomplex that makes a hollow shell. This TcB-TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB-TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.
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Affiliation(s)
- Jason N. Busby
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Sarah Trevelyan
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Cassandra L. Pegg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Edward D. Kerr
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Irene Chassagnon
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Michael J. Landsberg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Mitchell K. Weston
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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Rechiche O, Lee TV, Lott JS. Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography. Acta Crystallogr F Struct Biol Commun 2021; 77:334-340. [PMID: 34605437 PMCID: PMC8488854 DOI: 10.1107/s2053230x21009195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
The Ca2+-dependent enzyme peptidyl-arginine deiminase type III (PAD3) catalyses the deimination of arginine residues to form citrulline residues in proteins such as keratin, filaggrin and trichohyalin. This is an important post-translation modification that is required for normal hair and skin formation in follicles and keratocytes. The structure of apo human PAD3 was determined by X-ray crystallography to a resolution of 2.8 Å. The structure of PAD3 revealed a similar overall architecture to other PAD isoforms: the N-terminal and middle domains of PAD3 show sequence and structural variety, whereas the sequence and structure of the C-terminal catalytic domain is highly conserved. Structural analysis indicates that PAD3 is a dimer in solution, as is also the case for the PAD2 and PAD4 isoforms but not the PAD1 isoform.
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Affiliation(s)
- Othman Rechiche
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Althouse Laboratory, Science Drive, State College, PA 16801, USA
| | - T. Verne Lee
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
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Deshpande S, Altermann E, Sarojini V, Lott JS, Lee TV. Structural characterization of a PCP-R didomain from an archaeal nonribosomal peptide synthetase reveals novel interdomain interactions. J Biol Chem 2021; 296:100432. [PMID: 33610550 PMCID: PMC8024701 DOI: 10.1016/j.jbc.2021.100432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that produce a wide range of bioactive peptides, such as siderophores, toxins, and antibacterial and insecticidal agents. NRPSs are dynamic proteins characterized by extensive interdomain communications as a consequence of their assembly-line mode of synthesis. Hence, crystal structures of multidomain fragments of NRPSs have aided in elucidating crucial interdomain interactions that occur during different steps of the NRPS catalytic cycle. One crucial yet unexplored interaction is that between the reductase (R) domain and the peptide carrier protein (PCP) domain. R domains are members of the short-chain dehydrogenase/reductase family and function as termination domains that catalyze the reductive release of the final peptide product from the terminal PCP domain of the NRPS. Here, we report the crystal structure of an archaeal NRPS PCP-R didomain construct. This is the first NRPS R domain structure to be determined together with the upstream PCP domain and is also the first structure of an archaeal NRPS to be reported. The structure reveals that a novel helix-turn-helix motif, found in NRPS R domains but not in other short-chain dehydrogenase/reductase family members, plays a major role in the interface between the PCP and R domains. The information derived from the described PCP-R interface will aid in gaining further mechanistic insights into the peptide termination reaction catalyzed by the R domain and may have implications in engineering NRPSs to synthesize novel peptide products.
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Affiliation(s)
- Sandesh Deshpande
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Eric Altermann
- AgResearch Limited, Food System Integrity, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | | | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - T Verne Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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4
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McGregor R, Whitcombe AL, Sheen CR, Dickson JM, Day CL, Carlton LH, Sharma P, Lott JS, Koch B, Bennett J, Baker MG, Ritchie SR, Fox-Lewis S, Morpeth SC, Taylor SL, Roberts SA, Webb RH, Moreland NJ. Collaborative networks enable the rapid establishment of serological assays for SARS-CoV-2 during nationwide lockdown in New Zealand. PeerJ 2020; 8:e9863. [PMID: 32953275 PMCID: PMC7474877 DOI: 10.7717/peerj.9863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Serological assays that detect antibodies to SARS-CoV-2 are critical for determining past infection and investigating immune responses in the COVID-19 pandemic. We established ELISA-based immunoassays using locally produced antigens when New Zealand went into a nationwide lockdown and the supply chain of diagnostic reagents was a widely held domestic concern. The relationship between serum antibody binding measured by ELISA and neutralising capacity was investigated using a surrogate viral neutralisation test (sVNT). METHODS A pre-pandemic sera panel (n = 113), including respiratory infections with symptom overlap with COVID-19, was used to establish assay specificity. Sera from PCR‑confirmed SARS-CoV-2 patients (n = 21), and PCR-negative patients with respiratory symptoms suggestive of COVID-19 (n = 82) that presented to the two largest hospitals in Auckland during the lockdown period were included. A two-step IgG ELISA based on the receptor binding domain (RBD) and spike protein was adapted to determine seropositivity, and neutralising antibodies that block the RBD/hACE‑2 interaction were quantified by sVNT. RESULTS The calculated cut-off (>0.2) in the two-step ELISA maximised specificity by classifying all pre-pandemic samples as negative. Sera from all PCR-confirmed COVID-19 patients were classified as seropositive by ELISA ≥7 days after symptom onset. There was 100% concordance between the two-step ELISA and the sVNT with all 7+ day sera from PCR‑confirmed COVID-19 patients also classified as positive with respect to neutralising antibodies. Of the symptomatic PCR-negative cohort, one individual with notable travel history was classified as positive by two-step ELISA and sVNT, demonstrating the value of serology in detecting prior infection. CONCLUSIONS These serological assays were established and assessed at a time when human activity was severely restricted in New Zealand. This was achieved by generous sharing of reagents and technical expertise by the international scientific community, and highly collaborative efforts of scientists and clinicians across the country. The assays have immediate utility in supporting clinical diagnostics, understanding transmission in high-risk cohorts and underpinning longer‑term 'exit' strategies based on effective vaccines and therapeutics.
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Affiliation(s)
- Reuben McGregor
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
| | - Alana L. Whitcombe
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
| | - Campbell R. Sheen
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - James M. Dickson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Catherine L. Day
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lauren H. Carlton
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Prachi Sharma
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - J. Shaun Lott
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Barbara Koch
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - Julie Bennett
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Michael G. Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Stephen R. Ritchie
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Infectious Diseases Department, Auckland City Hospital, Auckland, New Zealand
| | - Shivani Fox-Lewis
- Department of Microbiology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | | | | | - Sally A. Roberts
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
- Department of Microbiology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Rachel H. Webb
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Starship Children’s Hospital, Auckland, New Zealand
| | - Nicole J. Moreland
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
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Abstract
Renal Na+ reabsorption, facilitated by the epithelial Na+ channel (ENaC), is subject to multiple forms of control to ensure optimal body blood volume and pressure through altering both the ENaC population and activity at the cell surface. Here, the focus is on regulating the number of ENaCs present in the apical membrane domain through pathways of ENaC synthesis and targeting to the apical membrane as well as ENaC removal, recycling, and degradation. Finally, the mechanisms by which ENaC trafficking pathways are regulated are summarized.
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Affiliation(s)
- Adam W Ware
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sahib R Rasulov
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tanya T Cheung
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Fiona J McDonald
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Piper SJ, Brillault L, Rothnagel R, Croll TI, Box JK, Chassagnon I, Scherer S, Goldie KN, Jones SA, Schepers F, Hartley-Tassell L, Ve T, Busby JN, Dalziel JE, Lott JS, Hankamer B, Stahlberg H, Hurst MRH, Landsberg MJ. Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin. Nat Commun 2019; 10:1952. [PMID: 31028251 PMCID: PMC6486591 DOI: 10.1038/s41467-019-09890-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 04/05/2019] [Indexed: 11/15/2022] Open
Abstract
ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen Yersinia entomophaga. Here we present cryo-EM structures of YenTcA, purified from the native source. The soluble pre-pore structure, determined at an average resolution of 4.4 Å, reveals a pentameric assembly that in contrast to other characterised ABC toxins is formed by two TcA-like proteins (YenA1 and YenA2) and decorated by two endochitinases (Chi1 and Chi2). We also identify conformational changes that accompany membrane pore formation by visualising YenTcA inserted into liposomes. A clear outward rotation of the Chi1 subunits allows for access of the protruding translocation pore to the membrane. Our results highlight structural and functional diversity within the ABC toxin subfamily, explaining how different ABC toxins are capable of recognising diverse hosts. YenTcA is the pore-forming and membrane binding subunit of the ABC toxin YenTc, which is produced by the insect pathogen Yersinia entomophaga. Here authors present cryo-EM structures of YenTcA purified from the native source which implicate associated endochitinases in host cell recognition.
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Affiliation(s)
- Sarah J Piper
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland, 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland, 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Rosalba Rothnagel
- Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Tristan I Croll
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge Cambridgeshire, CB2 0XY, United Kingdom
| | - Joseph K Box
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Irene Chassagnon
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Sebastian Scherer
- Centre for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4058, Basel, Switzerland
| | - Kenneth N Goldie
- Centre for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4058, Basel, Switzerland
| | - Sandra A Jones
- Forage Science Group, AgResearch, Christchurch, 8140, New Zealand
| | - Femke Schepers
- Faculty of Science, Leiden University, 2300 RA, Leiden, The Netherlands.,Food & Bio-based Products Group, AgResearch, Palmerston North, 4442, New Zealand
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Gold Coast Queensland, 4222, Australia
| | - Jason N Busby
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Julie E Dalziel
- Food & Bio-based Products Group, AgResearch, Palmerston North, 4442, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland, 4072, Australia
| | - Henning Stahlberg
- Centre for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, 4058, Basel, Switzerland
| | - Mark R H Hurst
- Forage Science Group, AgResearch, Christchurch, 8140, New Zealand
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Queensland, 4072, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia Queensland, 4072, Australia.
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7
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Jackson VA, Busby JN, Janssen BJC, Lott JS, Seiradake E. Teneurin Structures Are Composed of Ancient Bacterial Protein Domains. Front Neurosci 2019; 13:183. [PMID: 30930731 PMCID: PMC6425310 DOI: 10.3389/fnins.2019.00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
Pioneering bioinformatic analysis using sequence data revealed that teneurins evolved from bacterial tyrosine-aspartate (YD)-repeat protein precursors. Here, we discuss how structures of the C-terminal domain of teneurins, determined using X-ray crystallography and electron microscopy, support the earlier findings on the proteins’ ancestry. This chapter describes the structure of the teneurin scaffold with reference to a large family of teneurin-like proteins that are widespread in modern prokaryotes. The central scaffold of modern eukaryotic teneurins is decorated by additional domains typically found in bacteria, which are re-purposed in eukaryotes to generate highly multifunctional receptors. We discuss how alternative splicing contributed to further diversifying teneurin structure and thereby function. This chapter traces the evolution of teneurins from a structural point of view and presents the state-of-the-art of how teneurin function is encoded by its specific structural features.
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Affiliation(s)
| | - Jason N Busby
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - J Shaun Lott
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Nurul Islam M, Hitchings R, Kumar S, Fontes FL, Lott JS, Kruh-Garcia NA, Crick DC. Mechanism of Fluorinated Anthranilate-Induced Growth Inhibition in Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:55-62. [PMID: 30406991 DOI: 10.1021/acsinfecdis.8b00092] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biosynthesis of tryptophan in Mycobacterium tuberculosis is initiated by the transformation of chorismate to anthranilate, catalyzed by anthranilate synthase (TrpE/TrpG). Five additional enzymes are required to complete tryptophan biosynthesis. M. tuberculosis strains auxotrophic for tryptophan, an essential amino acid in the human diet, are avirulent. Thus, tryptophan synthesis in M. tuberculosis has been suggested as a potential drug target, and it has been reported that fluorinated anthranilate is lethal to the bacillus. Two mechanisms that could explain the cellular toxicity were tested: (1) the inhibition of tryptophan biosynthesis by a fluorinated intermediate or (2) formation of fluorotryptophan and its subsequent effects. Here, M. tuberculosis mc2 6230 cultures were treated with anthranilates fluorinated at positions 4, 5, and 6. These compounds inhibited bacterial growth on tryptophan-free media with 4-fluoroanthranilate being more potent than 5-fluoroanthranilate or 6-fluoroanthranilate. LC-MS based analysis of extracts from bacteria treated with these compounds did not reveal accumulation of any of the expected fluorinated intermediates in tryptophan synthesis. However, in all cases, significant levels of fluorotryptophan were readily observed, suggesting that the enzymes involved in the conversion of fluoro-anthranilate to fluorotryptophan were not being inhibited. Inclusion of tryptophan in cultures treated with the fluoro-anthranilates obviated the cellular toxicity. Bacterial growth was also inhibited in a dose-dependent manner by exposure to tryptophan substituted with fluorine at positions 5 or 6. Thus, the data suggest that fluorotryptophan rather than fluoro-anthranilate or intermediates in the synthesis of fluorotryptophan causes the inhibition of M. tuberculosis growth.
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Affiliation(s)
- M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Reese Hitchings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Fabio L. Fontes
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - J. Shaun Lott
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Nicole A. Kruh-Garcia
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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Upadhyay A, Kumar S, Rooker SA, Koehn JT, Crans DC, McNeil MR, Lott JS, Crick DC. Mycobacterial MenJ: An Oxidoreductase Involved in Menaquinone Biosynthesis. ACS Chem Biol 2018; 13:2498-2507. [PMID: 30091899 DOI: 10.1021/acschembio.8b00402] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
MenJ, annotated as an oxidoreductase, was recently demonstrated to catalyze the reduction (saturation) of a single double bond in the isoprenyl side-chain of mycobacterial menaquinone. This modification was shown to be essential for bacterial survival in J774A.1 macrophage-like cells, suggesting that MenJ may be a conditional drug target in Mycobacterium tuberculosis and other pathogenic mycobacteria. Recombinant protein was expressed in a heterologous host, and the activity was characterized. Although highly regiospecific in vivo, the activity is not absolutely regiospecific in vitro; in addition, the enzyme is not specific for naphthoquinones vs benzoquinones. Coenzyme Q-1 (a benzoquinone, UQ-1) was used as the lipoquinone substrate, and NADH oxidation was followed spectrophotometrically as the activity readout. NADPH could not be substituted for NADH in the reaction mixture. The enzyme contains a FAD binding site that was 72% occupied in the purified recombinant protein. Enzyme activity was maximal at 37 °C and pH 7.0; addition of divalent cations, EDTA, and reducing agents such as dithiothreitol to the reaction mixture had no effect on activity. The addition of detergents did not stimulate activity, and addition of saturating levels of FAD had relatively little effect on the observed kinetic parameters. These properties allowed the development of a facile assay needed to study this potential drug target, which is also amenable to high throughput screening. The Km values for UQ-1 using recombinant MenJ from Mycobacterium smegmatis or M. tuberculosis without saturating concentrations of FAD were found to be 52 ± 9.6 and 44 ± 4.8 μM, respectively, while the KmNADH values were determined to be 59 ± 14 and 64 ± 15 μM. The Km for MK-1, the menaquinone analogue of UQ-1, using recombinant MenJ from M. tuberculosis without saturating concentrations of FAD but in the presence of 0.5% Tween 80 was shown to be 30 ± 2.9 μM. Thus, this is the first report of a kinetic characterization of a member of the geranylgeranyl reductase family of enzymes.
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Affiliation(s)
- Ashutosh Upadhyay
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Steven A. Rooker
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Jordan T. Koehn
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Michael R. McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - J. Shaun Lott
- Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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10
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Healy MD, Hospenthal MK, Hall RJ, Chandra M, Chilton M, Tillu V, Chen KE, Celligoi DJ, McDonald FJ, Cullen PJ, Lott JS, Collins BM, Ghai R. Structural insights into the architecture and membrane interactions of the conserved COMMD proteins. eLife 2018; 7:e35898. [PMID: 30067224 PMCID: PMC6089597 DOI: 10.7554/elife.35898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.
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Affiliation(s)
- Michael D Healy
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | | | - Ryan J Hall
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Mintu Chandra
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - Vikas Tillu
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Kai-En Chen
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Dion J Celligoi
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | | | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - J Shaun Lott
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Rajesh Ghai
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
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11
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Rechiche O, Plowman JE, Harland DP, Lee TV, Lott JS. Expression and purification of high sulfur and high glycine-tyrosine keratin-associated proteins (KAPs) for biochemical and biophysical characterization. Protein Expr Purif 2018; 146:34-44. [DOI: 10.1016/j.pep.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 01/09/2023]
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12
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Evans GL, Furkert DP, Abermil N, Kundu P, de Lange KM, Parker EJ, Brimble MA, Baker EN, Lott JS. Datasets, processing and refinement details for Mtb-AnPRT: inhibitor structures with various space groups. Data Brief 2017; 15:1019-1029. [PMID: 29167811 PMCID: PMC5686470 DOI: 10.1016/j.dib.2017.10.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/21/2022] Open
Abstract
There are twenty-five published structures of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (Mtb-AnPRT) that use the same crystallization protocol. The structures include protein complexed with natural and alternative substrates, protein:inhibitor complexes, and variants with mutations of substrate-binding residues. Amongst these are varying space groups (i.e. P21, C2, P21212, P212121). This article outlines experimental details for 3 additional Mtb-AnPRT:inhibitor structures. For one protein:inhibitor complex, two datasets are presented – one generated by crystallization of protein in the presence of the inhibitor and another where a protein crystal was soaked with the inhibitor. Automatic and manual processing of these datasets indicated the same space group for both datasets and thus indicate that the space group differences between structures of Mtb-AnPRT:ligand complexes are not related to the method used to introduce the ligand.
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Affiliation(s)
- Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Daniel P Furkert
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Nacim Abermil
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Preeti Kundu
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Katrina M de Lange
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
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13
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Evans GL, Furkert DP, Abermil N, Kundu P, de Lange KM, Parker EJ, Brimble MA, Baker EN, Lott JS. Anthranilate phosphoribosyltransferase: Binding determinants for 5'-phospho-alpha-d-ribosyl-1'-pyrophosphate (PRPP) and the implications for inhibitor design. Biochim Biophys Acta Proteins Proteom 2017; 1866:264-274. [PMID: 28844746 DOI: 10.1016/j.bbapap.2017.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/07/2017] [Accepted: 08/07/2017] [Indexed: 12/17/2022]
Abstract
Phosphoribosyltransferases (PRTs) bind 5'-phospho-α-d-ribosyl-1'-pyrophosphate (PRPP) and transfer its phosphoribosyl group (PRib) to specific nucleophiles. Anthranilate PRT (AnPRT) is a promiscuous PRT that can phosphoribosylate both anthranilate and alternative substrates, and is the only example of a type III PRT. Comparison of the PRPP binding mode in type I, II and III PRTs indicates that AnPRT does not bind PRPP, or nearby metals, in the same conformation as other PRTs. A structure with a stereoisomer of PRPP bound to AnPRT from Mycobacterium tuberculosis (Mtb) suggests a catalytic or post-catalytic state that links PRib movement to metal movement. Crystal structures of Mtb-AnPRT in complex with PRPP and with varying occupancies of the two metal binding sites, complemented by activity assay data, indicate that this type III PRT binds a single metal-coordinated species of PRPP, while an adjacent second metal site can be occupied due to a separate binding event. A series of compounds were synthesized that included a phosphonate group to probe PRPP binding site. Compounds containing a "bianthranilate"-like moiety are inhibitors with IC50 values of 10-60μM, and Ki values of 1.3-15μM. Structures of Mtb-AnPRT in complex with these compounds indicate that their phosphonate moieties are unable to mimic the binding modes of the PRib or pyrophosphate moieties of PRPP. The AnPRT structures presented herein indicated that PRPP binds a surface cleft and becomes enclosed due to re-positioning of two mobile loops.
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Affiliation(s)
- Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand.
| | - Daniel P Furkert
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Nacim Abermil
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Preeti Kundu
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; Biomolecular Interaction Centre, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand; Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Katrina M de Lange
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; Biomolecular Interaction Centre, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand; Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand.
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14
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Gerth ML, Liu Y, Jiao W, Zhang XX, Baker EN, Lott JS, Rainey PB, Johnston JM. Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas. Proteins 2017; 85:1580-1588. [PMID: 28383128 DOI: 10.1002/prot.25303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/29/2017] [Accepted: 04/04/2017] [Indexed: 11/09/2022]
Abstract
Cupins form one of the most functionally diverse superfamilies of proteins, with members performing a wide range of catalytic, non-catalytic, and regulatory functions. HutD is a predicted bicupin protein that is involved in histidine utilization (Hut) in Pseudomonas species. Previous genetic analyses have suggested that it limits the upper level of Hut pathway expression, but its mechanism of action is unknown. Here, we have determined the structure of PfluHutD at 1.74 Å resolution in several crystallization conditions, and identified N-formyl-l-glutamate (FG, a Hut pathway intermediate) as a potential ligand in vivo. Proteins 2017; 85:1580-1588. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- M L Gerth
- New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand
| | - Y Liu
- New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand
| | - W Jiao
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - X-X Zhang
- New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand
| | - E N Baker
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand, New Zealand
| | - J S Lott
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand, New Zealand
| | - P B Rainey
- New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris Cedex 05, 75231, France.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thiennemann Strasse 2, Plön, 24306, Germany
| | - J M Johnston
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand, New Zealand
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15
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Busby JN, Lott JS, Panjikar S. Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure. Acta Crystallogr D Struct Biol 2016; 72:182-91. [PMID: 26894666 DOI: 10.1107/s2059798315023566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022]
Abstract
The B and C proteins from the ABC toxin complex of Yersinia entomophaga form a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12 data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used in Auto-Rickshaw for multiple rounds of autobuilding and MRSAD.
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Affiliation(s)
- Jason Nicholas Busby
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Santosh Panjikar
- MX, Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
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16
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Ho NAT, Dawes SS, Crowe AM, Casabon I, Gao C, Kendall SL, Baker EN, Eltis LD, Lott JS. The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis. J Biol Chem 2016; 291:7256-66. [PMID: 26858250 DOI: 10.1074/jbc.m115.707760] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
Cholesterol can be a major carbon source forMycobacterium tuberculosisduring infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma. KstR is a highly conserved TetR family transcriptional repressor that regulates a large set of genes responsible for cholesterol catabolism. Many genes in this regulon, includingkstR, are either induced during infection or are essential for survival ofM. tuberculosis in vivo In this study, we identified two ligands for KstR, both of which are CoA thioester cholesterol metabolites with four intact steroid rings. A metabolite in which one of the rings was cleaved was not a ligand. We confirmed the ligand-protein interactions using intrinsic tryptophan fluorescence and showed that ligand binding strongly inhibited KstR-DNA binding using surface plasmon resonance (IC50for ligand = 25 nm). Crystal structures of the ligand-free form of KstR show variability in the position of the DNA-binding domain. In contrast, structures of KstR·ligand complexes are highly similar to each other and demonstrate a position of the DNA-binding domain that is unfavorable for DNA binding. Comparison of ligand-bound and ligand-free structures identifies residues involved in ligand specificity and reveals a distinctive mechanism by which the ligand-induced conformational change mediates DNA release.
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Affiliation(s)
- Ngoc Anh Thu Ho
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Stephanie S Dawes
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Adam M Crowe
- the Departments of Biochemistry and Molecular Biology and
| | - Israël Casabon
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand, Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Chen Gao
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Sharon L Kendall
- the Department of Pathology and Pathogen Biology The Royal Veterinary College, Royal College Street, London NW1 0TU, United Kingdom, and
| | - Edward N Baker
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Lindsay D Eltis
- the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - J Shaun Lott
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand,
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17
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Cookson TVM, Evans GL, Castell A, Baker EN, Lott JS, Parker EJ. Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. Biochemistry 2016; 54:6082-92. [PMID: 26356348 DOI: 10.1021/acs.biochem.5b00612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Anthranilate phosphoribosyltransferase (AnPRT) is essential for the biosynthesis of tryptophan in Mycobacterium tuberculosis (Mtb). This enzyme catalyzes the second committed step in tryptophan biosynthesis, the Mg²⁺-dependent reaction between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and anthranilate. The roles of residues predicted to be involved in anthranilate binding have been tested by the analysis of six Mtb-AnPRT variant proteins. Kinetic analysis showed that five of six variants were active and identified the conserved residue R193 as being crucial for both anthranilate binding and catalytic function. Crystal structures of these Mtb-AnPRT variants reveal the ability of anthranilate to bind in three sites along an extended anthranilate tunnel and expose the role of the mobile β2-α6 loop in facilitating the enzyme's sequential reaction mechanism. The β2-α6 loop moves sequentially between a "folded" conformation, partially occluding the anthranilate tunnel, via an "open" position to a "closed" conformation, which supports PRPP binding and allows anthranilate access via the tunnel to the active site. The return of the β2-α6 loop to the "folded" conformation completes the catalytic cycle, concordantly allowing the active site to eject the product PRA and rebind anthranilate at the opening of the anthranilate tunnel for subsequent reactions. Multiple anthranilate molecules blocking the anthranilate tunnel prevent the β2-α6 loop from undergoing the conformational changes required for catalysis, thus accounting for the unusual substrate inhibition of this enzyme.
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Affiliation(s)
- Tammie V M Cookson
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
| | - Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Alina Castell
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
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18
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Bashiri G, Johnston JM, Evans GL, Bulloch EMM, Goldstone DC, Jirgis ENM, Kleinboelting S, Castell A, Ramsay RJ, Manos-Turvey A, Payne RJ, Lott JS, Baker EN. Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex. ACTA ACUST UNITED AC 2015; 71:2297-308. [DOI: 10.1107/s1399004715017216] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/14/2015] [Indexed: 01/16/2023]
Abstract
The tryptophan-biosynthesis pathway is essential for Mycobacterium tuberculosis (Mtb) to cause disease, but not all of the enzymes that catalyse this pathway in this organism have been identified. The structure and function of the enzyme complex that catalyses the first committed step in the pathway, the anthranilate synthase (AS) complex, have been analysed. It is shown that the open reading frames Rv1609 (trpE) and Rv0013 (trpG) encode the chorismate-utilizing (AS-I) and glutamine amidotransferase (AS-II) subunits of the AS complex, respectively. Biochemical assays show that when these subunits are co-expressed a bifunctional AS complex is obtained. Crystallization trials on Mtb-AS unexpectedly gave crystals containing only AS-I, presumably owing to its selective crystallization from solutions containing a mixture of the AS complex and free AS-I. The three-dimensional structure reveals that Mtb-AS-I dimerizes via an interface that has not previously been seen in AS complexes. As is the case in other bacteria, it is demonstrated that Mtb-AS shows cooperative allosteric inhibition by tryptophan, which can be rationalized based on interactions at this interface. Comparative inhibition studies on Mtb-AS-I and related enzymes highlight the potential for single inhibitory compounds to target multiple chorismate-utilizing enzymes for TB drug discovery.
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19
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Lee TV, Johnson RD, Arcus VL, Lott JS. Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening. Proteins 2015; 83:2052-66. [PMID: 26358936 DOI: 10.1002/prot.24922] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/19/2015] [Accepted: 08/28/2015] [Indexed: 12/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) synthesize a diverse array of bioactive small peptides, many of which are used in medicine. There is considerable interest in predicting NRPS substrate specificity in order to facilitate investigation of the many "cryptic" NRPS genes that have not been linked to any known product. However, the current sequence similarity-based methods are unable to produce reliable predictions when there is a lack of prior specificity data, which is a particular problem for fungal NRPSs. We conducted virtual screening on the specificity-determining domain of NRPSs, the adenylation domain, and found that virtual screening using experimentally determined structures results in good enrichment of the cognate substrate. Our results indicate that the conformation of the adenylation domain and in particular the conformation of a key conserved aromatic residue is important in determining the success of the virtual screening. When homology models of NRPS adenylation domains of known specificity, rather than experimentally determined structures, were built and used for virtual screening, good enrichment of the cognate substrate was also achieved in many cases. However, the accuracy of the models was key to the reliability of the predictions and there was a large variation in the results when different models of the same domain were used. This virtual screening approach is promising and is able to produce enrichment of the cognate substrates in many cases, but improvements in building and assessing homology models are required before the approach can be reliably applied to these models.
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Affiliation(s)
- T Verne Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard D Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Vickery L Arcus
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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20
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Stubbing LA, Lott JS, Dawes SS, Furkert DP, Brimble MA. Synthesis of DOHNAA, aMycobacterium tuberculosisCholesterol CD Ring Catabolite and FadD3 Substrate. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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21
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Chai AF, Bulloch EMM, Evans GL, Lott JS, Baker EN, Johnston JM. A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket. ACTA ACUST UNITED AC 2015; 71:862-72. [PMID: 25849397 DOI: 10.1107/s1399004715001650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/25/2015] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. Access to iron in host macrophages depends on iron-chelating siderophores called mycobactins and is strongly correlated with Mtb virulence. Here, the crystal structure of an Mtb enzyme involved in mycobactin biosynthesis, MbtN, in complex with its FAD cofactor is presented at 2.30 Å resolution. The polypeptide fold of MbtN conforms to that of the acyl-CoA dehydrogenase (ACAD) family, consistent with its predicted role of introducing a double bond into the acyl chain of mycobactin. Structural comparisons and the presence of an acyl carrier protein, MbtL, in the same gene locus suggest that MbtN acts on an acyl-(acyl carrier protein) rather than an acyl-CoA. A notable feature of the crystal structure is the tubular density projecting from N(5) of FAD. This was interpreted as a covalently bound polyethylene glycol (PEG) fragment and resides in a hydrophobic pocket where the substrate acyl group is likely to bind. The pocket could accommodate an acyl chain of 14-21 C atoms, consistent with the expected length of the mycobactin acyl chain. Supporting this, steady-state kinetics show that MbtN has ACAD activity, preferring acyl chains of at least 16 C atoms. The acyl-binding pocket adopts a different orientation (relative to the FAD) to other structurally characterized ACADs. This difference may be correlated with the apparent ability of MbtN to catalyse the formation of an unusual cis double bond in the mycobactin acyl chain.
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Affiliation(s)
- Ai-Fen Chai
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Esther M M Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Genevieve L Evans
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jodie M Johnston
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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22
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Evans GL, Gamage SA, Bulloch EMM, Baker EN, Denny WA, Lott JS. Corrigendum: Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis in Mycobacterium tuberculosis. Chembiochem 2015; 16:706. [DOI: 10.1002/cbic.201500098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Dawes SS, Kendall SL, Baker EN, Lott JS. Purification, crystallization and preliminary X-ray crystallographic studies of KstR2 (ketosteroid regulatory protein) from Mycobacterium tuberculosis. Acta Crystallogr F Struct Biol Commun 2014; 70:1643-5. [PMID: 25484217 PMCID: PMC4259231 DOI: 10.1107/s2053230x14023589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/27/2014] [Indexed: 11/10/2022] Open
Abstract
KstR2 (Rv3557c) is one of two TetR-family transcriptional repressors of cholesterol metabolism in Mycobacterium tuberculosis. The ability to degrade cholesterol fully is important for pathogenesis, and therefore this repressor was expressed, purified and crystallized. Crystals of KstR2 diffracted to better than 1.9 Å resolution and belonged to space group C2, with unit-cell parameters a = 72.3, b = 90.3, c = 49.7 Å, α = γ = 90, β = 128.2°.
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Affiliation(s)
- Stephanie S. Dawes
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Sharon L. Kendall
- Pathology and Pathogen Biology, The Royal Veterinary College, Royal College Street, London NW1 0TU, England
| | - Edward N. Baker
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J. Shaun Lott
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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24
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Evans GL, Gamage SA, Bulloch EMM, Baker EN, Denny WA, Lott JS. Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis inMycobacterium tuberculosis. Chembiochem 2014; 15:852-64. [DOI: 10.1002/cbic.201300628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Indexed: 11/10/2022]
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25
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Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, Cook GM. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Mol Microbiol 2014; 91:950-64. [PMID: 24444429 DOI: 10.1111/mmi.12507] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2013] [Indexed: 11/30/2022]
Abstract
Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5 Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.
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Affiliation(s)
- Adam Heikal
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
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26
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Chai AF, Johnston JM, Bunker RD, Bulloch EMM, Evans GL, Lott JS, Baker EN. Purification, crystallization and preliminary X-ray studies of MbtN (Rv1346) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1354-1356. [PMID: 24316828 PMCID: PMC3855718 DOI: 10.1107/s1744309113027000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/01/2013] [Indexed: 06/02/2023]
Abstract
In Mycobacterium tuberculosis, the protein MbtN (Rv1346) catalyzes the formation of a double bond in the fatty-acyl moiety of the siderophore mycobactin, which is used by this organism to acquire essential iron. MbtN is homologous to acyl-CoA dehydrogenases, whose general role is to catalyze the α,β-dehydrogenation of fatty-acyl-CoA conjugates. Mycobactins, however, contain a long unsaturated fatty-acid chain with an unusual cis double bond conjugated to the carbonyl group of the mycobactin core. To characterize the role of MbtN in the dehydrogenation of this fatty-acyl moiety, the enzyme has been expressed, purified and crystallized. The crystals diffracted to 2.3 Å resolution at a synchrotron source and were found to belong to the hexagonal space group H32, with unit-cell parameters a = b = 139.10, c = 253.09 Å, α = β = 90, γ = 120°.
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Affiliation(s)
- Ai Fen Chai
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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27
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Busby JN, Panjikar S, Landsberg MJ, Hurst MRH, Lott JS. The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device. Nature 2013; 501:547-50. [PMID: 23913273 DOI: 10.1038/nature12465] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/16/2013] [Indexed: 12/20/2022]
Abstract
The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity and potential role in human disease. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic. The carboxy-terminal region of the C protein is the main cytotoxic component, and is poorly conserved between different toxin complexes. A general model of action has been proposed, in which the toxin complex binds to the cell surface via the A protein, is endocytosed, and subsequently forms a pH-triggered channel, allowing the translocation of C into the cytoplasm, where it can cause cytoskeletal disruption in both insect and mammalian cells. Toxin complexes have been visualized using single-particle electron microscopy, but no high-resolution structures of the components are available, and the role of the B protein in the mechanism of toxicity remains unknown. Here we report the three-dimensional structure of the complex formed between the B and C proteins, determined to 2.5 Å by X-ray crystallography. These proteins assemble to form an unprecedented, large hollow structure that encapsulates and sequesters the cytotoxic, C-terminal region of the C protein like the shell of an egg. The shell is decorated on one end by a β-propeller domain, which mediates attachment of the B-C heterodimer to the A protein in the native complex. The structure reveals how C auto-proteolyses when folded in complex with B. The C protein is the first example, to our knowledge, of a structure that contains rearrangement hotspot (RHS) repeats, and illustrates a marked structural architecture that is probably conserved across both this widely distributed bacterial protein family and the related eukaryotic tyrosine-aspartate (YD)-repeat-containing protein family, which includes the teneurins. The structure provides the first clues about the function of these protein repeat families, and suggests a generic mechanism for protein encapsulation and delivery.
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Affiliation(s)
- Jason N Busby
- AgResearch Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
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28
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Bobby R, Medini K, Neudecker P, Lee TV, Brimble MA, McDonald FJ, Lott JS, Dingley AJ. Structure and dynamics of human Nedd4-1 WW3 in complex with the αENaC PY motif. Biochim Biophys Acta 2013; 1834:1632-41. [PMID: 23665454 DOI: 10.1016/j.bbapap.2013.04.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) is an E3 ubiquitin ligase that interacts with and negatively regulates the epithelial Na(+) channel (ENaC). The WW domains of Nedd4-1 bind to the ENaC subunits via recognition of PY motifs. Human Nedd4-1 (hNedd4-1) contains four WW domains with the third domain (WW3*) showing the strongest affinity to the PY motif. To understand the mechanism underlying this binding affinity, we have carried out NMR structural and dynamics analyses of the hNedd4-1 WW3* domain in complex with a peptide comprising the C-terminal tail of the human ENaC α-subunit. The structure reveals that the peptide interacts in a similar manner to other WW domain-ENaC peptide structures. Crucial interactions that likely provide binding affinity are the broad XP groove facilitating additional contacts between the WW3* domain and the peptide, compared to similar complexes, and the large surface area buried (83Å(2)) between R430 (WW3*) and L647' (αENaC). This corroborates the model-free analysis of the (15)N backbone relaxation data, which showed that R430 is the most rigid residue in the domain (S(2)=0.90±0.01). Carr-Purcell-Meiboom-Gill relaxation dispersion analysis identified two different conformational exchange processes on the μs-ms time-scale. One of these processes involves residues located at the peptide binding interface, suggesting conformational exchange may play a role in peptide recognition. Thus, both structural and dynamic features of the complex appear to define the high binding affinity. The results should aid interpretation of biochemical data and modeling interfaces between Nedd4-1 and other interacting proteins.
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Affiliation(s)
- Romel Bobby
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
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29
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Castell A, Short FL, Evans GL, Cookson TVM, Bulloch EMM, Joseph DDA, Lee CE, Parker EJ, Baker EN, Lott JS. The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition. Biochemistry 2013; 52:1776-87. [DOI: 10.1021/bi301387m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alina Castell
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Francesca L. Short
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Genevieve L. Evans
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Tammie V. M. Cookson
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Esther M. M. Bulloch
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Dmitri D. A. Joseph
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Clare E. Lee
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Edward N. Baker
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J. Shaun Lott
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
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30
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Chi G, Manos-Turvey A, O’Connor PD, Johnston JM, Evans GL, Baker EN, Payne RJ, Lott JS, Bulloch EMM. Implications of Binding Mode and Active Site Flexibility for Inhibitor Potency against the Salicylate Synthase from Mycobacterium tuberculosis. Biochemistry 2012; 51:4868-79. [DOI: 10.1021/bi3002067] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Gamma Chi
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | | | - Patrick D. O’Connor
- Auckland Cancer Society Research
Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jodie M. Johnston
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Genevieve L. Evans
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Edward N. Baker
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - J. Shaun Lott
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
| | - Esther M. M. Bulloch
- School of Biological Sciences
and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private
Bag 92019, Auckland 1142, New Zealand
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31
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Koulman A, Lee TV, Fraser K, Johnson L, Arcus V, Lott JS, Rasmussen S, Lane G. Identification of extracellular siderophores and a related peptide from the endophytic fungus Epichloë festucae in culture and endophyte-infected Lolium perenne. Phytochemistry 2012; 75:128-39. [PMID: 22196939 PMCID: PMC3311397 DOI: 10.1016/j.phytochem.2011.11.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 11/17/2011] [Accepted: 11/29/2011] [Indexed: 05/10/2023]
Abstract
A number of genes encoding non-ribosomal peptide synthetases (NRPSs) have been identified in fungi of Epichloë/Neotyphodium species, endophytes of Pooid grasses, including sidN, putatively encoding a ferrichrome siderophore-synthesizing NRPS. Targeted gene replacement and complementation of sidN in Epichloë festucae has established that extracellular siderophore epichloënin A is the major product of the SidN enzyme complex (Johnson et al., 2007a). We report here high resolution mass spectrometric fragmentation experiments and NMR analysis of an isolated fraction establishing that epichloënin A is a siderophore of the ferrichrome family, comprising a cyclic sequence of four glycines, a glutamine and three N(δ)-trans-anhydromevalonyl-N(δ)-hydroxyornithine (AMHO) moieties. Epichloënin A is unusual among ferrichrome siderophores in comprising an octapeptide rather than hexapeptide sequence, and in incorporating a glutamine residue. During this investigation we have established that desferrichrome siderophores with pendant trans-AMHO groups can be distinguished from those with pendant cis-AMHO groups by the characteristic neutral loss of an hydroxyornithine moiety in the MS/MS spectrum. A minor component, epichloënin B, has been characterized as the triglycine variant by mass spectrometry. A peptide characterized by mass spectrometry as the putative deoxygenation product, epichloëamide has been detected together with ferriepichloënin A in guttation fluid from ryegrass (Lolium perenne) plants infected with wild-type E. festucae, but not in plants infected with the ΔsidN mutant strain, and also detected at trace levels in wild-type E. festucae fungal culture.
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Affiliation(s)
- Albert Koulman
- Lipid Profiling and Signaling Group, MRC HNR, Elsie Widdowson Laboratory, Cambridge, UK
| | - T. Verne Lee
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Karl Fraser
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Linda Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Vickery Arcus
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand
| | - J. Shaun Lott
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Susanne Rasmussen
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Geoffrey Lane
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
- Corresponding author. Address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North 4442, New Zealand. Tel.: +64 6 356 8019; fax: +64 6 351 8032.
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Manos-Turvey A, Cergol KM, Salam NK, Bulloch EMM, Chi G, Pang A, Britton WJ, West NP, Baker EN, Lott JS, Payne RJ. Synthesis and evaluation of M. tuberculosis salicylate synthase (MbtI) inhibitors designed to probe plasticity in the active site. Org Biomol Chem 2012; 10:9223-36. [DOI: 10.1039/c2ob26736e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Landsberg MJ, Jones SA, Rothnagel R, Busby JN, Marshall SDG, Simpson RM, Lott JS, Hankamer B, Hurst MRH. 3D structure of the Yersinia entomophaga toxin complex and implications for insecticidal activity. Proc Natl Acad Sci U S A 2011; 108:20544-9. [PMID: 22158901 PMCID: PMC3251104 DOI: 10.1073/pnas.1111155108] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Toxin complex (Tc) proteins are a class of bacterial protein toxins that form large, multisubunit complexes. Comprising TcA, B, and C components, they are of great interest because many exhibit potent insecticidal activity. Here we report the structure of a novel Tc, Yen-Tc, isolated from the bacterium Yersinia entomophaga MH96, which differs from the majority of bacterially derived Tcs in that it exhibits oral activity toward a broad range of insect pests, including the diamondback moth (Plutella xylostella). We have determined the structure of the Yen-Tc using single particle electron microscopy and studied its mechanism of toxicity by comparative analyses of two variants of the complex exhibiting different toxicity profiles. We show that the A subunits form the basis of a fivefold symmetric assembly that differs substantially in structure and subunit arrangement from its most well characterized homologue, the Xenorhabdus nematophila toxin XptA1. Histopathological and quantitative dose response analyses identify the B and C subunits, which map to a single, surface-accessible region of the structure, as the sole determinants of toxicity. Finally, we show that the assembled Yen-Tc has endochitinase activity and attribute this to putative chitinase subunits that decorate the surface of the TcA scaffold, an observation that may explain the oral toxicity associated with the complex.
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Affiliation(s)
- Michael J. Landsberg
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sandra A. Jones
- Innovative Farming Systems, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Rosalba Rothnagel
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jason N. Busby
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; and
| | - Sean D. G. Marshall
- Innovative Farming Systems, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Robert M. Simpson
- New Zealand Institute for Plant and Food Research, Palmerston North 4474, New Zealand
| | - J. Shaun Lott
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand; and
| | - Ben Hankamer
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark R. H. Hurst
- Innovative Farming Systems, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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35
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Manos-Turvey A, Bulloch EMM, Rutledge PJ, Baker EN, Lott JS, Payne RJ. Inhibition studies of Mycobacterium tuberculosis salicylate synthase (MbtI). ChemMedChem 2010; 5:1067-79. [PMID: 20512795 DOI: 10.1002/cmdc.201000137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis salicylate synthase (MbtI), a member of the chorismate-utilizing enzyme family, catalyses the first committed step in the biosynthesis of the siderophore mycobactin T. This complex secondary metabolite is essential for both virulence and survival of M. tuberculosis, the etiological agent of tuberculosis (TB). It is therefore anticipated that inhibitors of this enzyme may serve as TB therapies with a novel mode of action. Herein we describe the first inhibition study of M. tuberculosis MbtI using a library of functionalized benzoate-based inhibitors designed to mimic the substrate (chorismate) and intermediate (isochorismate) of the MbtI-catalyzed reaction. The most potent inhibitors prepared were those designed to mimic the enzyme intermediate, isochorismate. These compounds, based on a 2,3-dihydroxybenzoate scaffold, proved to be low-micromolar inhibitors of MbtI. The most potent inhibitors in this series possessed hydrophobic enol ether side chains at C3 in place of the enol-pyruvyl side chain found in chorismate and isochorismate.
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36
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Lee TV, Lott JS, Johnson RD, Arcus VL. Expression and purification of an adenylation domain from a eukaryotic nonribosomal peptide synthetase: using structural genomics tools for a challenging target. Protein Expr Purif 2010; 74:162-8. [PMID: 20716446 DOI: 10.1016/j.pep.2010.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 08/04/2010] [Accepted: 08/11/2010] [Indexed: 10/19/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multimodular and multidomain enzymes that are involved in synthesising an array of molecules that are important in human and animal health. NRPSs are found in both bacteria and fungi but most of the research to date has focused on the bacterial enzymes. This is largely due to the technical challenges in producing active fungal NRPSs, which stem from their large size and multidomain nature. In order to target fungal NRPS domains for biochemical and structural characterisation, we tackled this challenge by using the cloning and expression tools of structural genomics to screen the many variables that can influence the expression and purification of proteins. Using these tools we have screened 32 constructs containing 16 different fungal NRPS domains or domain combinations for expression and solubility. Two of these yielded soluble protein with one, the third adenylation domain of the SidN NRPS (SidNA3) from the grass endophyte Neotyphodium lolii, being tractable for purification using Ni-affinity resin. The initial purified protein exhibited poor solution behaviour but optimisation of the expression construct and the buffer conditions used for purification, resulted in stable recombinant protein suitable for biochemical characterisation, crystallisation and structure determination.
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Affiliation(s)
- T Verne Lee
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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37
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Kendall SL, Burgess P, Balhana R, Withers M, ten Bokum A, Lott JS, Gao C, Uhia-Castro I, Stoker NG. Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2. Microbiology (Reading) 2010; 156:1362-1371. [PMID: 20167624 PMCID: PMC3068626 DOI: 10.1099/mic.0.034538-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 01/21/2010] [Accepted: 02/12/2010] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis is able to use a variety of carbon sources in vivo and current knowledge suggests that cholesterol is used as a carbon source during infection. The catabolized cholesterol is used both as an energy source (ATP generation) and as a source of precursor molecules for the synthesis of complex methyl-branched fatty acids. In previous studies, we described a TetR-type transcriptional repressor, kstR, that controls the expression of a number of genes involved in cholesterol catabolism. In this study, we describe a second TetR-type repressor, which we call kstR2. We knocked this gene out in Mycobacterium smegmatis and used microarrays and quantitative RT-PCR to examine the effects on gene expression. We identified a palindromic regulatory motif for KstR2, showed that this motif is present in three promoter regions in mycobacteria and rhodococcus, and demonstrated binding of purified KstR2 to the motif. Using a combination of motif location analysis, gene expression analysis and the examination of gene conservation, we suggest that kstR2 controls the expression of a 15 gene regulon. Like kstR, kstR2 and the kstR2 regulon are highly conserved among the actinomycetes and studies in rhodococcus suggest a role for these genes in cholesterol catabolism. The functional significance of the regulon and implications for the control of cholesterol utilization are discussed.
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Affiliation(s)
- Sharon L. Kendall
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - Philippa Burgess
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - Ricardo Balhana
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - Mike Withers
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - Annemieke ten Bokum
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - J. Shaun Lott
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, New Zealand
| | - Chen Gao
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, New Zealand
| | - Iria Uhia-Castro
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Neil G. Stoker
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Centre for Emerging, Endemic and Exotic Disease, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
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Lee TV, Johnson LJ, Johnson RD, Koulman A, Lane GA, Lott JS, Arcus VL. Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. J Biol Chem 2009; 285:2415-27. [PMID: 19923209 DOI: 10.1074/jbc.m109.071324] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. We report the structure of the third adenylation domain from the siderophore-synthesizing NRPS, SidN, from the endophytic fungus Neotyphodium lolii. This is the first structure of a eukaryotic NRPS domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, N(delta)-cis-anhydromevalonyl-N(delta)-hydroxy-L-ornithine (cis-AMHO). The specific activation of cis-AMHO was confirmed biochemically, and an AMHO moiety was unambiguously identified as a component of the fungal siderophore using mass spectroscopy. The protein structure shows that the substrate binding pocket is defined by 17 amino acid residues, in contrast to both prokaryotic adenylation domains and to previous predictions based on modeling. Existing substrate prediction methods for NRPS adenylation domains fail for domains from eukaryotes due to the divergence of their signature sequences from those of prokaryotes. Thus, this new structure will provide a basis for improving prediction methods for eukaryotic NRPS enzymes that play important and diverse roles in the biology of fungi.
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Affiliation(s)
- T Verne Lee
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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Moreland NJ, Charlier C, Dingley AJ, Baker EN, Lott JS. Making sense of a missense mutation: characterization of MutT2, a Nudix hydrolase from Mycobacterium tuberculosis, and the G58R mutant encoded in W-Beijing strains of M. tuberculosis. Biochemistry 2009; 48:699-708. [PMID: 19115962 DOI: 10.1021/bi8009554] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent polymorphism analyses of Mycobacterium tuberculosis strains have identified missense mutations unique to the W-Beijing lineage in genes belonging to the Nudix hydrolase superfamily. This study investigates the structure and function of one of these Nudix hydrolases, MutT2, and examines the effect that the W-Beijing mutation (G58R) has on enzyme characteristics. MutT2 has a preference for cytidine triphosphates, and although the G58R mutation does not alter nucleotide specificity, it reduces the protein's affinity for divalent cations. The K(D) of free Mg(2+) is 79-fold higher for the G58R mutant (3.30 +/- 0.19 mM) compared with that for the wild-type (41.7 +/- 1.4 microM). Circular dichroism and nuclear magnetic resonance spectroscopy measurements show that while the mutation does not perturb the overall structure of the protein, protein stability is significantly compromised by the presence of the arginine with DeltaG (H(2)O), the free-energy of unfolding, being reduced by 2.48 kcal mol(-1) in the G58R mutant. Homology modeling of MutT2 shows that Gly-58 is in close proximity (10.8 A) to the Mg(2+) binding site formed by the highly conserved Nudix box residues and hydrogen bonds with Ala-54 in the preceding alpha-helix. This may explain the increased divalent cation requirement and decreased stability observed when an arginine is substituted for glycine at this position. A role for MutT2 in the regulation of cytidine-triphosphates available for nucleotide-dependent reactions is postulated, and the impact that the G58R mutation may have on these reactions is discussed.
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Affiliation(s)
- Nicole J Moreland
- Maurice Wilkins Centre for Molecular Biodiscovery and Laboratory of Structural Biology, School of Biological Sciences, University of Auckland, New Zealand.
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Sharpe ML, Gao C, Kendall SL, Baker EN, Lott JS. The Structure and Unusual Protein Chemistry of Hypoxic Response Protein 1, a Latency Antigen and Highly Expressed Member of the DosR Regulon in Mycobacterium tuberculosis. J Mol Biol 2008; 383:822-36. [DOI: 10.1016/j.jmb.2008.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 01/20/2023]
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Goldstone RM, Moreland NJ, Bashiri G, Baker EN, Shaun Lott J. A new Gateway vector and expression protocol for fast and efficient recombinant protein expression in Mycobacterium smegmatis. Protein Expr Purif 2007; 57:81-7. [PMID: 17949993 DOI: 10.1016/j.pep.2007.08.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Revised: 08/09/2007] [Accepted: 08/13/2007] [Indexed: 11/16/2022]
Abstract
A major obstacle associated with recombinant protein over-expression in Escherichia coli is the production of insoluble inclusion bodies, a problem particularly pronounced with Mycobacterium tuberculosis proteins. One strategy to overcome the formation of inclusion bodies is to use an expression host that is more closely related to the organism from which the proteins are derived. Here we describe methods for efficiently identifying M. tuberculosis proteins that express in soluble form in Mycobacterium smegmatis. We have adapted the M. smegmatis expression vector pYUB1049 to the Gateway cloning system by the addition of att recombination recognition sequences. The resulting vector, designated pDESTsmg, is compatible with our in-house Gateway methods for E. coli expression. A target can be subcloned into pDESTsmg by a simple LR reaction using an entry clone generated for E. coli expression, removing the need to design new primers and re-clone target DNA. Proteins are expressed by culturing the M. smegmatis strain mc(2)4517 in autoinduction media supplemented with Tween 80. The media used are the same as those used for expression of proteins in E. coli, simplifying and reducing the cost of the switch to an alternative host. The methods have been applied to a set of M. tuberculosis proteins that form inclusion bodies when expressed in E. coli. We found that five of eight of these previously insoluble proteins become soluble when expressed in M. smegmatis, demonstrating that this is an efficient salvage strategy.
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Affiliation(s)
- Rachael M Goldstone
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, Thomas Building, 3a Symonds Street, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Kendall SL, Withers M, Soffair CN, Moreland NJ, Gurcha S, Sidders B, Frita R, ten Bokum A, Besra GS, Lott JS, Stoker NG. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol Microbiol 2007; 65:684-99. [PMID: 17635188 PMCID: PMC1995591 DOI: 10.1111/j.1365-2958.2007.05827.x] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Mycobacterium tuberculosis TetR-type regulator Rv3574 has been implicated in pathogenesis as it is induced in vivo, and genome-wide essentiality studies show it is required for infection. As the gene is highly conserved in the mycobacteria, we deleted the Rv3574 orthologue in Mycobacterium smegmatis (MSMEG_6042) and used real-time quantitative polymerase chain reaction and microarray analyses to show that it represses the transcription both of itself and of a large number of genes involved in lipid metabolism. We identified a conserved motif within its own promoter (TnnAACnnGTTnnA) and showed that it binds as a dimer to 29 bp probes containing the motif. We found 16 and 31 other instances of the motif in intergenic regions of M. tuberculosis and M. smegmatis respectively. Combining the results of the microarray studies with the motif analyses, we predict that Rv3574 directly controls the expression of 83 genes in M. smegmatis, and 74 in M. tuberculosis. Many of these genes are known to be induced by growth on cholesterol in rhodococci, and palmitate in M. tuberculosis. We conclude that this regulator, designated elsewhere as kstR, controls the expression of genes used for utilizing diverse lipids as energy sources, possibly imported through the mce4 system.
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Affiliation(s)
- Sharon L Kendall
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
| | - Mike Withers
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
| | - Catherine N Soffair
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
| | - Nicole J Moreland
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of AucklandAuckland, New Zealand.
| | - Sudagar Gurcha
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK.
| | - Ben Sidders
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
| | - Rosangela Frita
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
| | - Annemieke ten Bokum
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon WC1E 7HT, UK.
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK.
| | - J Shaun Lott
- Laboratory of Structural Biology and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of AucklandAuckland, New Zealand.
| | - Neil G Stoker
- Department of Pathology and Infectious Diseases, The Royal Veterinary CollegeRoyal College Street, London NW1 0TU, UK.
- For correspondence. E-mail: ; Tel. (+020) 7468 5272; Fax (+020) 7468 5306
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Murillo AC, Li HY, Alber T, Baker EN, Berger JM, Cherney LT, Cherney MM, Cho YS, Eisenberg D, Garen CR, Goulding CW, Hung LW, Ioerger TR, Jacobs WR, James MNG, Kim C, Krieger I, Lott JS, Sankaranarayanan R, Segelke BW, Terwilliger TC, Wang F, Wang S, Sacchettini JC. High throughput crystallography of TB drug targets. Infect Disord Drug Targets 2007; 7:127-139. [PMID: 17970224 DOI: 10.2174/187152607781001853] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Tuberculosis (TB) infects one-third of the world population. Despite 50 years of available drug treatments, TB continues to increase at a significant rate. The failure to control TB stems in part from the expense of delivering treatment to infected individuals and from complex treatment regimens. Incomplete treatment has fueled the emergence of multi-drug resistant (MDR) strains of Mycobacterium tuberculosis (Mtb). Reducing non-compliance by reducing the duration of chemotherapy will have a great impact on TB control. The development of new drugs that either kill persisting organisms, inhibit bacilli from entering the persistent phase, or convert the persistent bacilli into actively growing cells susceptible to our current drugs will have a positive effect. We are taking a multidisciplinary approach that will identify and characterize new drug targets that are essential for persistent Mtb. Targets are exposed to a battery of analyses including microarray experiments, bioinformatics, and genetic techniques to prioritize potential drug targets from Mtb for structural analysis. Our core structural genomics pipeline works with the individual laboratories to produce diffraction quality crystals of targeted proteins, and structural analysis will be completed by the individual laboratories. We also have capabilities for functional analysis and the virtual ligand screening to identify novel inhibitors for target validation. Our overarching goals are to increase the knowledge of Mtb pathogenesis using the TB research community to drive structural genomics, particularly related to persistence, develop a central repository for TB research reagents, and discover chemical inhibitors of drug targets for future development of lead compounds.
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Affiliation(s)
- A C Murillo
- Texas A&M University, Department of Biochemistry and Biophysics, College Station 77843-2128, USA
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Harrison AJ, Yu M, Gårdenborg T, Middleditch M, Ramsay RJ, Baker EN, Lott JS. The structure of MbtI from Mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase. J Bacteriol 2006; 188:6081-91. [PMID: 16923875 PMCID: PMC1595383 DOI: 10.1128/jb.00338-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 06/21/2006] [Indexed: 11/20/2022] Open
Abstract
The ability to acquire iron from the extracellular environment is a key determinant of pathogenicity in mycobacteria. Mycobacterium tuberculosis acquires iron exclusively via the siderophore mycobactin T, the biosynthesis of which depends on the production of salicylate from chorismate. Salicylate production in other bacteria is either a two-step process involving an isochorismate synthase (chorismate isomerase) and a pyruvate lyase, as observed for Pseudomonas aeruginosa, or a single-step conversion catalyzed by a salicylate synthase, as with Yersinia enterocolitica. Here we present the structure of the enzyme MbtI (Rv2386c) from M. tuberculosis, solved by multiwavelength anomalous diffraction at a resolution of 1.8 A, and biochemical evidence that it is the salicylate synthase necessary for mycobactin biosynthesis. The enzyme is critically dependent on Mg2+ for activity and produces salicylate via an isochorismate intermediate. MbtI is structurally similar to salicylate synthase (Irp9) from Y. enterocolitica and the large subunit of anthranilate synthase (TrpE) and shares the overall architecture of other chorismate-utilizing enzymes, such as the related aminodeoxychorismate synthase PabB. Like Irp9, but unlike TrpE or PabB, MbtI is neither regulated by nor structurally stabilized by bound tryptophan. The structure of MbtI is the starting point for the design of inhibitors of siderophore biosynthesis, which may make useful lead compounds for the production of new antituberculosis drugs, given the strong dependence of pathogenesis on iron acquisition in M. tuberculosis.
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Affiliation(s)
- Anthony J Harrison
- Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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Lott JS, Paget B, Johnston JM, Delbaere LTJ, Sigrell-Simon JA, Banfield MJ, Baker EN. The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine-specific kinases. J Biol Chem 2006; 281:22131-22141. [PMID: 16737961 DOI: 10.1074/jbc.m603062200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation of both small molecules and proteins plays a central role in many biological processes. In proteins, phosphorylation most commonly targets the oxygen atoms of Ser, Thr, and Tyr. In contrast, stably phosphorylated His residues are rarely found, due to the lability of the N-P bond, and histidine phosphorylation features most often in transient processes. Here we present the crystal structure of a protein of previously unknown function, which proves to contain a stably phosphorylated histidine residue. The protein is the product of open reading frame PAE2307, from the hyperthermophilic archaeon Pyrobaculum aerophilum, and is representative of a highly conserved protein family found in archaea and bacteria. The crystal structure of PAE2307, solved at 1.45-A resolution (R = 0.208, R(free) = 0.227), forms a remarkably tightly associated hexamer. The phosphorylated histidine at the proposed active site, pHis85, occupies a cavity that is at the interface between two subunits and contains a number of fully conserved residues. Stable phosphorylation is attributed to favorable hydrogen bonding of the phosphoryl group and a salt bridge with pHis85 that provides electronic stabilization. In silico modeling suggested that the protein may function as an adenosine kinase, a conclusion that is supported by in vitro assays of adenosine binding, using fluorescence spectroscopy, and crystallographic visualization of an adenosine complex of PAE2307 at 2.25-A resolution.
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Affiliation(s)
- J Shaun Lott
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Blake Paget
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Jodie M Johnston
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Louis T J Delbaere
- Department of Biochemistry, University of Saskatchewan, Saskatoon S7N 5E5, Canada
| | - Jill A Sigrell-Simon
- Department of Research and Development, GE Healthcare, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Mark J Banfield
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Edward N Baker
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand.
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Lee CE, Goodfellow C, Javid-Majd F, Baker EN, Shaun Lott J. The Crystal Structure of TrpD, a Metabolic Enzyme Essential for Lung Colonization by Mycobacterium tuberculosis, in Complex with its Substrate Phosphoribosylpyrophosphate. J Mol Biol 2006; 355:784-97. [PMID: 16337227 DOI: 10.1016/j.jmb.2005.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 11/02/2005] [Accepted: 11/06/2005] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis, the cause of tuberculosis, presents a major threat to human health worldwide. Biosynthetic enzymes that are essential for the survival of the bacterium, especially in activated macrophages, are important potential drug targets. Although the tryptophan biosynthesis pathway is thought to be non-essential for many pathogens, this appears not to be the case for M.tuberculosis, where a trpD gene knockout fails to cause disease in mice. We therefore chose the product of the trpD gene, anthranilate phosphoribosyltransferase, which catalyses the second step in tryptophan biosynthesis, for structural analysis. The structure of TrpD from M.tuberculosis was solved by X-ray crystallography, at 1.9 A resolution for the native enzyme (R = 0.191, Rfree = 0.230) and at 2.3 A resolution for the complex with its substrate phosphoribosylpyrophosphate (PRPP) and Mg2+ (R = 0.194, Rfree = 0.255). The enzyme is folded into two domains, separated by a hinge region. PRPP binds in the C-terminal domain, together with a pair of Mg ions. In the substrate complex, two flexible loops change conformation compared with the apo protein, to close over the PRPP and to complete an extensive network of hydrogen-bonded interactions. A nearby pocket, adjacent to the hinge region, is postulated by in silico docking as the binding site for anthranilate. A bound molecule of benzamidine, which was essential for crystallization and is also found in the hinge region, appears to reduce flexibility between the two domains.
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Affiliation(s)
- Clare E Lee
- Laboratory of Structural Biology and Centre for Molecular Biodiscovery, School of Biological Sciences University of Auckland, Private Bag 92019, Auckland 1020, New Zealand
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Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans, is a devastating infectious organism that kills approximately two million people annually. The current suite of antibiotics used to treat TB faces two main difficulties: (i) the emergence of multidrug-resistant (MDR) strains of M. tuberculosis, and (ii) the persistent state of the bacterium, which is less susceptible to antibiotics and causes very long antibiotic treatment regimes. The complete genome sequences of a laboratory strain (H37Rv) and a clinical strain (CDC1551) of M. tuberculosis and the concurrent identification of all the open reading frames that encode proteins within this organism, present structural biologists with a wide array of protein targets for structure determination. Comparative genomics of the species that make up the M. tuberculosis complex has also added an array of genomic information to our understanding of these organisms. In response to this, structural genomics consortia have been established for targeting proteins from M. tuberculosis. This review looks at the progress of these major initiatives and the potential impact of large scale structure determination efforts on the development of inhibitors to many proteins. Increasing sophistication in structure-based drug design approaches, in combination with increasing numbers of protein structures and inhibitors for TB proteins, will have a significant impact on the downstream development of TB antibiotics.
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Affiliation(s)
- Vickery L Arcus
- AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, New Zealand.
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48
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Webby CJ, Baker HM, Lott JS, Baker EN, Parker EJ. The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes. J Mol Biol 2005; 354:927-39. [PMID: 16288916 DOI: 10.1016/j.jmb.2005.09.093] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/28/2022]
Abstract
The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties.
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Affiliation(s)
- Celia J Webby
- Centre of Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Moreland N, Ashton R, Baker HM, Ivanovic I, Patterson S, Arcus VL, Baker EN, Lott JS. A flexible and economical medium-throughput strategy for protein production and crystallization. Acta Crystallogr D Biol Crystallogr 2005; 61:1378-85. [PMID: 16204890 DOI: 10.1107/s0907444905023590] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 07/25/2005] [Indexed: 11/11/2022]
Abstract
Large-scale structural genomics centres rely heavily on robotics to ensure that maximum throughput is achieved. However, the size and cost of these approaches is out of the reach of most academic structural biology efforts. A major challenge for such groups is to adapt current high-throughput schemes to a reasonable scale with the resources available. A flexible medium-throughput approach has been developed that is suitable for typical academic research groups. Following nested PCR, targets are routinely cloned into two Gateway expression vectors (pDEST15 for an N-terminal GST tag and pDEST17 for an N-terminal His tag). Expression of soluble recombinant protein in Escherichia coli is rapidly assessed in 96-well format. An eight-probe sonicator is utilized and a six-buffer lysis screen was incorporated to enhance solubility. Robotics is reserved for crystallization, since this is the key bottleneck for crystallography. Screening proteins with a 480-condition protocol using a Cartesian nanolitre-dispensing robot has increased crystallization success markedly, with an overall success rate (structures solved out of proteins screened) of 19%. The methods are robust and economical -- with the exception of the crystallization robot, investment in additional equipment has been minimal at 9000 US dollars. All protocols are designed for individuals so that graduate students and postdoctoral fellows gain expertise in every aspect of the structural pipeline, from cloning to crystallization.
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Affiliation(s)
- Nicole Moreland
- School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, New Zealand.
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50
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Sharpe ML, Baker EN, Lott JS. Crystallization of a protein using dehydration without a precipitant. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:565-8. [PMID: 16511097 PMCID: PMC1952335 DOI: 10.1107/s1744309105014235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 05/03/2005] [Indexed: 11/10/2022]
Abstract
Hypoxic response protein I (HRPI) is a protein of unknown biochemical function whose expression is very strongly upregulated in response to oxygen depletion in Mycobacterium tuberculosis. Crystals have been grown from a solution of full-length HRPI by the unusual method of dehydration without the use of precipitants. The crystals produced diffract to a maximum resolution of 2.1 A and belong to space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters a = b = 79.18, c = 37.34 A.
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Affiliation(s)
- Miriam L Sharpe
- School of Biological Sciences, Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland 1003, New Zealand.
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