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Waksman T, Astin E, Fisher SR, Hunter WN, Bos JIB. Computational Prediction of Structure, Function, and Interaction of Myzus persicae (Green Peach Aphid) Salivary Effector Proteins. Mol Plant Microbe Interact 2024; 37:338-346. [PMID: 38171380 DOI: 10.1094/mpmi-10-23-0154-fi] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Similar to plant pathogens, phloem-feeding insects such as aphids deliver effector proteins inside their hosts that act to promote host susceptibility and enable feeding and infestation. Despite exciting progress toward identifying and characterizing effector proteins from these insects, their functions remain largely unknown. The recent groundbreaking development in protein structure prediction algorithms, combined with the availability of proteomics and transcriptomic datasets for agriculturally important pests, provides new opportunities to explore the structural and functional diversity of effector repertoires. In this study, we sought to gain insight into the infection strategy used by the Myzus persicae (green peach aphid) by predicting and analyzing the structures of a set of 71 effector candidate proteins. We used two protein structure prediction methods, AlphaFold and OmegaFold, that produced mutually consistent results. We observed a wide continuous spectrum of structures among the effector candidates, from disordered proteins to globular enzymes. We made use of the structural information and state-of-the-art computational methods to predict M. persicae effector protein properties, including function and interaction with host plant proteins. Overall, our investigation provides novel insights into prediction of structure, function, and interaction of M. persicae effector proteins and will guide the necessary experimental characterization to address new hypotheses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Thomas Waksman
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Edmund Astin
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - S Ronan Fisher
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - William N Hunter
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Jorunn I B Bos
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, U.K
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Hagan M, Pankov G, Gallegos-Monterrosa R, Williams DJ, Earl C, Buchanan G, Hunter WN, Coulthurst SJ. Rhs NADase effectors and their immunity proteins are exchangeable mediators of inter-bacterial competition in Serratia. Nat Commun 2023; 14:6061. [PMID: 37770429 PMCID: PMC10539506 DOI: 10.1038/s41467-023-41751-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Many bacterial species use Type VI secretion systems (T6SSs) to deliver anti-bacterial effector proteins into neighbouring bacterial cells, representing an important mechanism of inter-bacterial competition. Specific immunity proteins protect bacteria from the toxic action of their own effectors, whilst orphan immunity proteins without a cognate effector may provide protection against incoming effectors from non-self competitors. T6SS-dependent Rhs effectors contain a variable C-terminal toxin domain (CT), with the cognate immunity protein encoded immediately downstream of the effector. Here, we demonstrate that Rhs1 effectors from two strains of Serratia marcescens, the model strain Db10 and clinical isolate SJC1036, possess distinct CTs which both display NAD(P)+ glycohydrolase activity but belong to different subgroups of NADase from each other and other T6SS-associated NADases. Comparative structural analysis identifies conserved functions required for NADase activity and reveals that unrelated NADase immunity proteins utilise a common mechanism of effector inhibition. By replicating a natural recombination event, we show successful functional exchange of CTs and demonstrate that Db10 encodes an orphan immunity protein which provides protection against T6SS-delivered SJC1036 NADase. Our findings highlight the flexible use of Rhs effectors and orphan immunity proteins during inter-strain competition and the repeated adoption of NADase toxins as weapons against bacterial cells.
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Affiliation(s)
- Martin Hagan
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Genady Pankov
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | | | - David J Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Christopher Earl
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - William N Hunter
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Sarah J Coulthurst
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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Pankov G, Mol Avelar G, Buchanan G, Coulthurst SJ, Hunter WN. The structure of a tautomerase superfamily member linked to the type VI secretion system of Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2023; 79:8-16. [PMID: 36598351 PMCID: PMC9813972 DOI: 10.1107/s2053230x22011414] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteria exploit specialized secretion systems to assist in competition for resources, in collaboration and in communication. Here, a protocol for the recombinant production, purification and crystallization of a protein linked to the Acinetobacter baumannii type VI secretion system is provided. A high-resolution structure of this trimeric protein is reported, revealing the characteristic dual β-α-β subunit fold typical of longer subunit members of the tautomerase superfamily. The protein does not appear to be toxic to bacteria or yeast under the conditions tested. The possible biological role of this protein is discussed.
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Affiliation(s)
- Genady Pankov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Gabriela Mol Avelar
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Grant Buchanan
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Sarah J. Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom,Correspondence e-mail:
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Parker HP, Dawson A, Jones MJ, Yan R, Ouyang J, Hong R, Hunter WN. Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (−)-hosieine-A. Acta Crystallogr F Struct Biol Commun 2022; 78:313-323. [PMID: 36048081 PMCID: PMC9435674 DOI: 10.1107/s2053230x22007762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
The affinity and thermodynamic parameters for the interactions of two naturally occurring neurotoxins, (+)-anatoxin-a and (−)-hosieine-A, with acetylcholine-binding protein were investigated using a fluorescence-quenching assay and isothermal titration calorimetry. The crystal structures of their complexes with acetylcholine-binding protein from Aplysia californica (AcAChBP) were determined and reveal details of molecular recognition in the orthosteric binding site. Comparisons treating AcAChBP as a surrogate for human α4β2 and α7 nicotinic acetylcholine receptors (nAChRs) suggest that the molecular features involved in ligand recognition and affinity for the protein targets are conserved. The ligands exploit interactions with similar residues as the archetypal nAChR agonist nicotine, but with greater affinity. (−)-Hosieine-A in particular has a high affinity for AcAChBP driven by a favorable entropic contribution to binding. The ligand affinities help to rationalize the potent biological activity of these alkaloids. The structural data, together with comparisons with related molecules, suggest that there may be opportunities to extend the hosieine-A scaffold to incorporate new interactions with the complementary side of the orthosteric binding site. Such a strategy may guide the design of new entities to target human α4β2 nAChR that may have therapeutic benefit.
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Bueno RV, Davis S, Dawson A, Ondachi PW, Carroll FI, Hunter WN. Interactions between 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors. Acta Crystallogr D Struct Biol 2022; 78:353-362. [PMID: 35234149 PMCID: PMC8900824 DOI: 10.1107/s2059798322000754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 11/29/2022] Open
Abstract
The binding of a series of epibatidine derivatives to acetylcholine-binding protein was investigated using biolayer interferometry. The structures of three complexes inform discussion on the biological implications for interactions with nicotinic acetylcholine receptor subtypes, which are important targets for control of pain. Low-nanomolar binding constants were recorded for a series of six 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues with acetylcholine-binding protein (AChBP). The crystal structures of three complexes with AChBP reveal details of molecular recognition in the orthosteric binding site and imply how the other three ligands bind. Comparisons exploiting AChBP as a surrogate for α4β2 and α7 nicotinic acetylcholine receptors (nAChRs) suggest that the key interactions are conserved. The ligands interact with the same residues as the archetypal nAChR agonist nicotine yet display greater affinity, thereby rationalizing their in vivo activity as potent antagonists of nicotine-induced antinociception. An oxyanion-binding site is formed on the periphery of the AChBP orthosteric site by Lys42, Asp94, Glu170 and Glu210. These residues are highly conserved in the human α4, β2 and α7 nAChR sequences. However, specific sequence differences are discussed that could contribute to nAChR subtype selectivity and in addition may represent a point of allosteric modulation. The ability to engage with this peripheral site may explain, in part, the function of a subset of ligands to act as agonists of α7 nAChR.
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Jones MJ, Dawson A, Hales TG, Hunter WN. A Structural Rationale for N-Methylbicuculline Acting as a Promiscuous Competitive Antagonist of Inhibitory Pentameric Ligand-Gated Ion Channels. Chembiochem 2020; 21:1526-1533. [PMID: 31859406 DOI: 10.1002/cbic.201900680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 11/07/2022]
Abstract
Bicuculline, a valued chemical tool in neurosciences research, is a competitive antagonist of specific GABAA receptors and affects other pentameric ligand-gated ion channels including the glycine, nicotinic acetylcholine and 5-hydroxytryptamine type 3 receptors. We used a fluorescence-quenching assay and isothermal titration calorimetry to record low-micromolar dissociation constants for N-methylbicuculline interacting with acetylcholine-binding protein and an engineered version called glycine-binding protein (GBP), which provides a surrogate for the heteromeric interface of the extracellular domain of the glycine receptor (GlyR). The 2.4 Å resolution crystal structure of the GBP:N-methylbicuculline complex, sequence and structural alignments reveal similarities and differences between GlyR and the GABAA receptor-bicuculline interactions. N-methylbicuculline displays a similar conformation in different structures, but adopts distinct orientations enforced by interactions and steric blocks with key residues and plasticity in the binding sites. These features explain the promiscuous activity of bicuculline against the principal inhibitory pentameric ligand-gated ion channels in the CNS.
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Affiliation(s)
- Mathew J Jones
- Division of Biological Chemistry and Drug Discovery School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Alice Dawson
- Division of Biological Chemistry and Drug Discovery School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
| | - Tim G Hales
- Division of Systems Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee, DD1 9SY, UK
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK
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Davis S, Rego Campello H, Gallagher T, Hunter WN. The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica. Acta Crystallogr F Struct Biol Commun 2020; 76:74-80. [PMID: 32039888 PMCID: PMC7010356 DOI: 10.1107/s2053230x20001168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/21/2019] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP-4 complex indicated close similarities in the protein-ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.
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Affiliation(s)
- Samuel Davis
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | | | - Timothy Gallagher
- School of Chemistry, University of Bristol, Bristol BS8 1TS, England
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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Dawson A, Trumper P, de Souza JO, Parker H, Jones MJ, Hales TG, Hunter WN. Engineering a surrogate human heteromeric α/β glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. IUCrJ 2019; 6:1014-1023. [PMID: 31709057 PMCID: PMC6830221 DOI: 10.1107/s205225251901114x] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Protein-engineering methods have been exploited to produce a surrogate system for the extracellular neurotransmitter-binding site of a heteromeric human ligand-gated ion channel, the glycine receptor. This approach circumvents two major issues: the inherent experimental difficulties in working with a membrane-bound ion channel and the complication that a heteromeric assembly is necessary to create a key, physiologically relevant binding site. Residues that form the orthosteric site in a highly stable ortholog, acetylcholine-binding protein, were selected for substitution. Recombinant proteins were prepared and characterized in stepwise fashion exploiting a range of biophysical techniques, including X-ray crystallography, married to the use of selected chemical probes. The decision making and development of the surrogate, which is termed a glycine-binding protein, are described, and comparisons are provided with wild-type and homomeric systems that establish features of molecular recognition in the binding site and the confidence that the system is suited for use in early-stage drug discovery targeting a heteromeric α/β glycine receptor.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Paul Trumper
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Juliana Oliveira de Souza
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Holly Parker
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Mathew J. Jones
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Tim G. Hales
- Division of Systems Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Díaz-Sáez L, Torrie LS, McElroy SP, Gray D, Hunter WN. Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. FEBS J 2019; 286:4509-4524. [PMID: 31260169 PMCID: PMC6899670 DOI: 10.1111/febs.14976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023]
Abstract
Burkholderia pseudomallei is a serious, difficult to treat Gram‐negative pathogen and an increase in the occurrence of drug‐resistant strains has been detected. We have directed efforts to identify and to evaluate potential drug targets relevant to treatment of infection by B. pseudomallei. We have selected and characterised the essential enzyme d‐alanine‐d‐alanine ligase (BpDdl), required for the ATP‐assisted biosynthesis of a peptidoglycan precursor. A recombinant supply of protein supported high‐resolution crystallographic and biophysical studies with ligands (AMP and AMP+d‐Ala‐d‐Ala), and comparisons with orthologues enzymes suggest a ligand‐induced conformational change occurring that might be relevant to the catalytic cycle. The detailed biochemical characterisation of the enzyme, development and optimisation of ligand binding assays supported the search for novel inhibitors by screening of selected compound libraries. In a similar manner to that observed previously in other studies, we note a paucity of hits that are worth follow‐up and then in combination with a computational analysis of the active site, we conclude that this ligase represents a difficult target for drug discovery. Nevertheless, our reagents, protocols and data can underpin future efforts exploiting more diverse chemical libraries and structure‐based approaches.
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Affiliation(s)
- Laura Díaz-Sáez
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, UK
| | - Leah S Torrie
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, UK
| | - Stuart P McElroy
- European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - David Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, UK
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, UK
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Pankov G, Dawson A, Hunter WN. The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2019; 75:227-232. [PMID: 30950822 DOI: 10.1107/s2053230x19001778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022]
Abstract
The thick outer membrane (OM) of Gram-negative bacteria performs an important protective role against hostile environments, supports cell integrity, and contributes to surface adhesion and in some cases also to virulence. A major component of the OM is lipopolysaccharide (LPS), a complex glycolipid attached to a core containing fatty-acyl chains. The assembly and transport of lipid A, the membrane anchor for LPS, to the OM begins when a heteromeric LptB2FG protein complex extracts lipid A from the outer leaflet of the inner membrane. This process requires energy, and upon hydrolysis of ATP one component of the heteromeric assembly, LptB, triggers a conformational change in LptFG in support of lipid A transport. A structure of LptB from the intracellular pathogen Burkholderia pseudomallei is reported here. LptB forms a dimer that displays a relatively fixed structure irrespective of whether it is in complex with LptFG or in isolation. Highly conserved sequence and structural features are discussed that allow LptB to fuel the transport of lipid A.
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Affiliation(s)
- Genady Pankov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Alice Dawson
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Bueno R, Dawson A, Hunter WN. An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase-ligand complexes following further refinement. Acta Crystallogr F Struct Biol Commun 2019; 75:148-152. [PMID: 30839287 DOI: 10.1107/s2053230x18018083] [Citation(s) in RCA: 2] [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: 08/10/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022]
Abstract
The enzymes involved in folate metabolism are key drug targets for cell-growth modulation, and accurate crystallographic structures provide templates to be exploited for structure-based ligand design. In this context, three ternary complex structures of human methylenetetrahydrofolate dehydrogenase/cyclohydrolase have been published [Schmidt et al. (2000), Biochemistry, 39, 6325-6335] and potentially represent starting points for the development of new antifolate inhibitors. However, an inspection of the models and the deposited data revealed deficiencies and raised questions about the validity of the structures. A number of inconsistencies relating to the publication were also identified. Additional refinement was carried out with the deposited data, seeking to improve the models and to then validate the complex structures or correct the record. In one case, the inclusion of the inhibitor in the structure was supported and alterations to the model allowed details of enzyme-ligand interactions to be described that had not previously been discussed. For one weak inhibitor, the data suggested that the ligand may adopt two poses in the binding site, both with few interactions with the enzyme. In the third case, that of a potent inhibitor, inconsistencies were noted in the assignment of the chemical structure and there was no evidence to support the inclusion of the ligand in the active site.
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Affiliation(s)
- Renata Bueno
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Gottschald Chiodi C, Baptista-Hon DT, Hunter WN, Hales TG. Amino acid substitutions in the human homomeric β 3 GABA A receptor that enable activation by GABA. J Biol Chem 2018; 294:2375-2385. [PMID: 30545943 DOI: 10.1074/jbc.ra118.006229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/04/2018] [Indexed: 11/06/2022] Open
Abstract
GABAA receptors (GABAARs) are pentameric ligand-gated ion channels that mediate synaptic inhibition throughout the central nervous system. The α1β2γ2 receptor is the major subtype in the brain; GABA binds at the β2(+)α1(-) interface. The structure of the homomeric β3 GABAAR, which is not activated by GABA, has been solved. Recently, four additional heteromeric structures were reported, highlighting key residues required for agonist binding. Here, we used a protein engineering method, taking advantage of knowledge of the key binding residues, to create a β3(+)α1(-) heteromeric interface in the homomeric human β3 GABAAR that enables GABA-mediated activation. Substitutions were made in the complementary side of the orthosteric binding site in loop D (Y87F and Q89R), loop E (G152T), and loop G (N66D and A70T). The Q89R and G152T combination enabled low-potency activation by GABA and potentiation by propofol but impaired direct activation by higher propofol concentrations. At higher concentrations, GABA inhibited gating of β3 GABAAR variants containing Y87F, Q89R, and G152T. Reversion of Phe87 to tyrosine abolished GABA's inhibitory effect and partially recovered direct activation by propofol. This tyrosine is conserved in homomeric GABAARs and in the Erwinia chrysanthemi ligand-gated ion channel and may be essential for the absence of an inhibitory effect of GABA on homomeric channels. This work demonstrated that only two substitutions, Q89R and G152T, in β3 GABAAR are sufficient to reconstitute GABA-mediated activation and suggests that Tyr87 prevents inhibitory effects of GABA.
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Affiliation(s)
- Carla Gottschald Chiodi
- From Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom and
| | - Daniel T Baptista-Hon
- The Institute of Academic Anaesthesia, Division of Systems Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - William N Hunter
- From Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom and
| | - Tim G Hales
- The Institute of Academic Anaesthesia, Division of Systems Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
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Linciano P, Dawson A, Pöhner I, Costa DM, Sá MS, Cordeiro-da-Silva A, Luciani R, Gul S, Witt G, Ellinger B, Kuzikov M, Gribbon P, Reinshagen J, Wolf M, Behrens B, Hannaert V, Michels PAM, Nerini E, Pozzi C, di Pisa F, Landi G, Santarem N, Ferrari S, Saxena P, Lazzari S, Cannazza G, Freitas-Junior LH, Moraes CB, Pascoalino BS, Alcântara LM, Bertolacini CP, Fontana V, Wittig U, Müller W, Wade RC, Hunter WN, Mangani S, Costantino L, Costi MP. Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery. ACS Omega 2017; 2:5666-5683. [PMID: 28983525 PMCID: PMC5623949 DOI: 10.1021/acsomega.7b00473] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
Pteridine reductase-1 (PTR1) is a promising drug target for the treatment of trypanosomiasis. We investigated the potential of a previously identified class of thiadiazole inhibitors of Leishmania major PTR1 for activity against Trypanosoma brucei (Tb). We solved crystal structures of several TbPTR1-inhibitor complexes to guide the structure-based design of new thiadiazole derivatives. Subsequent synthesis and enzyme- and cell-based assays confirm new, mid-micromolar inhibitors of TbPTR1 with low toxicity. In particular, compound 4m, a biphenyl-thiadiazole-2,5-diamine with IC50 = 16 μM, was able to potentiate the antitrypanosomal activity of the dihydrofolate reductase inhibitor methotrexate (MTX) with a 4.1-fold decrease of the EC50 value. In addition, the antiparasitic activity of the combination of 4m and MTX was reversed by addition of folic acid. By adopting an efficient hit discovery platform, we demonstrate, using the 2-amino-1,3,4-thiadiazole scaffold, how a promising tool for the development of anti-T. brucei agents can be obtained.
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Affiliation(s)
- Pasquale Linciano
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Alice Dawson
- Biological Chemistry &
Drug Discovery, School of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Ina Pöhner
- Molecular
and Cellular Modeling Group and Scientific Databases and Visualization
(SDBV) Group, Heidelberg Institute for Theoretical
Studies, Schloss-Wolfsbrunnenweg
35, D-69118 Heidelberg, Germany
| | - David M. Costa
- Instituto de Investigação
e Inovação em Saúde, Instituto de Biologia Molecular
e Celular, and Departamento de Ciências Biológicas, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Monica S. Sá
- Instituto de Investigação
e Inovação em Saúde, Instituto de Biologia Molecular
e Celular, and Departamento de Ciências Biológicas, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Anabela Cordeiro-da-Silva
- Instituto de Investigação
e Inovação em Saúde, Instituto de Biologia Molecular
e Celular, and Departamento de Ciências Biológicas, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Rosaria Luciani
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Sheraz Gul
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Gesa Witt
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | | | - Maria Kuzikov
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | | | - Markus Wolf
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Birte Behrens
- Fraunhofer-IME SP, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Véronique Hannaert
- Research Unit for Tropical
Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Paul A. M. Michels
- Research Unit for Tropical
Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Erika Nerini
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Cecilia Pozzi
- University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Flavio di Pisa
- University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giacomo Landi
- University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Nuno Santarem
- Instituto de Investigação
e Inovação em Saúde, Instituto de Biologia Molecular
e Celular, and Departamento de Ciências Biológicas, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Stefania Ferrari
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Puneet Saxena
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Sandra Lazzari
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giuseppe Cannazza
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Lucio H. Freitas-Junior
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Carolina B. Moraes
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Bruno S. Pascoalino
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Laura M. Alcântara
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Claudia P. Bertolacini
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Vanessa Fontana
- Laboratório Nacional de Biociências CNPEM,
Centro Nacional de Pesquisa em Energia e Materials, Rua Giuseppe Máximo Scolfaro, 10.000, CEP 13083-970 Campinas/SP, Brasil
| | - Ulrike Wittig
- Molecular
and Cellular Modeling Group and Scientific Databases and Visualization
(SDBV) Group, Heidelberg Institute for Theoretical
Studies, Schloss-Wolfsbrunnenweg
35, D-69118 Heidelberg, Germany
| | - Wolfgang Müller
- Molecular
and Cellular Modeling Group and Scientific Databases and Visualization
(SDBV) Group, Heidelberg Institute for Theoretical
Studies, Schloss-Wolfsbrunnenweg
35, D-69118 Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular
and Cellular Modeling Group and Scientific Databases and Visualization
(SDBV) Group, Heidelberg Institute for Theoretical
Studies, Schloss-Wolfsbrunnenweg
35, D-69118 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ−ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany
| | - William N. Hunter
- Biological Chemistry &
Drug Discovery, School of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | | | - Luca Costantino
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Maria P. Costi
- Dipartimento di
Scienze della Vita, Università degli
Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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14
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Oliveira de Souza J, Dawson A, Hunter WN. An Improved Model of the Trypanosoma brucei CTP Synthetase Glutaminase Domain-Acivicin Complex. ChemMedChem 2017; 12:577-579. [PMID: 28333400 PMCID: PMC5413811 DOI: 10.1002/cmdc.201700118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 02/20/2017] [Revised: 03/21/2017] [Indexed: 11/17/2022]
Abstract
The natural product acivicin inhibits the glutaminase activity of cytidine triphosphate (CTP) synthetase and is a potent lead compound for drug discovery in the area of neglected tropical diseases, specifically trypanosomaisis. A 2.1-Å-resolution crystal structure of the acivicin adduct with the glutaminase domain from Trypanosoma brucei CTP synthetase has been deposited in the RCSB Protein Data Bank (PDB) and provides a template for structure-based approaches to design new inhibitors. However, our assessment of that data identified deficiencies in the model. We now report an improved and corrected inhibitor structure with changes to the chirality at one position, the orientation and covalent structure of the isoxazoline moiety, and the location of a chloride ion in an oxyanion binding site that is exploited during catalysis. The model is now in agreement with established chemical principles and allows an accurate description of molecular recognition of the ligand and the mode of binding in a potentially valuable drug target.
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Affiliation(s)
- Juliana Oliveira de Souza
- Division of Biological Chemistry and Drug DiscoveryCollege of Life SciencesUniversity of DundeeDundeeDD1 5EHScotlandUK
| | - Alice Dawson
- Division of Biological Chemistry and Drug DiscoveryCollege of Life SciencesUniversity of DundeeDundeeDD1 5EHScotlandUK
| | - William N. Hunter
- Division of Biological Chemistry and Drug DiscoveryCollege of Life SciencesUniversity of DundeeDundeeDD1 5EHScotlandUK
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15
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Díaz-Sáez L, Pankov G, Hunter WN. Open and compressed conformations of Francisella tularensis ClpP. Proteins 2016; 85:188-194. [PMID: 27802578 PMCID: PMC5225881 DOI: 10.1002/prot.25197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 07/25/2016] [Revised: 10/13/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022]
Abstract
Caseinolytic proteases are large oligomeric assemblies responsible for maintaining protein homeostasis in bacteria and in so doing influence a wide range of biological processes. The functional assembly involves three chaperones together with the oligomeric caseinolytic protease catalytic subunit P (ClpP). This protease represents a potential target for therapeutic intervention in pathogenic bacteria. Here, we detail an efficient protocol for production of recombinant ClpP from Francisella tularensis, and the structural characterization of three crystal forms which grow under similar conditions. One crystal form reveals a compressed state of the ClpP tetradecamer and two forms an open state. A comparison of the two types of structure infers that differences at the enzyme active site result from a conformational change involving a highly localized disorder‐order transition of a β‐strand α‐helix combination. This transition occurs at a subunit‐subunit interface. Our study may now underpin future efforts in a structure‐based approach to target ClpP for inhibitor or activator development. Proteins 2016; 85:188–194. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Laura Díaz-Sáez
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Genady Pankov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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16
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Wilson NJ, Cole C, Kroboth K, Hunter WN, Mann JA, McLean WHI, Kernland Lang K, Beltraminelli H, Sabroe RA, Tiffin N, Sobey GJ, Borradori L, Simpson E, Smith FJD. Mutations in POGLUT1 in Galli-Galli/Dowling-Degos disease. Br J Dermatol 2016; 176:270-274. [PMID: 27479915 PMCID: PMC5324688 DOI: 10.1111/bjd.14914] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- N J Wilson
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K
| | - C Cole
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K.,Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, U.K
| | - K Kroboth
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K
| | - W N Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K
| | - J A Mann
- Department of Dermatology, Oregon Health & Sciences University, Portland, OR, U.S.A.,Division of Dermatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, U.S.A
| | - W H I McLean
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K
| | - K Kernland Lang
- Department of Dermatology, University Hospital-Inselspital Bern, University of Bern, Bern, Switzerland
| | - H Beltraminelli
- Department of Dermatology, University Hospital-Inselspital Bern, University of Bern, Bern, Switzerland
| | - R A Sabroe
- Department of Dermatology, Royal Hallamshire Hospital, Sheffield, U.K
| | - N Tiffin
- Department of Histopathology, Royal Hallamshire Hospital, Sheffield, U.K
| | - G J Sobey
- Department of Clinical Genetics, Sheffield Children's Hospital, Sheffield, U.K
| | - L Borradori
- Department of Dermatology, University Hospital-Inselspital Bern, University of Bern, Bern, Switzerland
| | - E Simpson
- Department of Dermatology, Oregon Health & Sciences University, Portland, OR, U.S.A
| | - F J D Smith
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, U.K.,Pachyonychia Congenita Project, Salt Lake City, UT, U.S.A
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17
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Jäger F, Zoltner M, Kneuper H, Hunter WN, Palmer T. Membrane interactions and self-association of components of the Ess/Type VII secretion system of Staphylococcus aureus. FEBS Lett 2016; 590:349-57. [PMID: 26785823 PMCID: PMC4949537 DOI: 10.1002/1873-3468.12065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 12/03/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 01/03/2023]
Abstract
The Ess/Type VII protein secretion system, essential for virulence of pathogenic Staphylococcus aureus, is dependent upon the four core membrane proteins EssA, EssB, EssC and EsaA. Here, we use crosslinking and blue native PAGE analysis to show that the EssB, EssC and EsaA proteins individually form homomeric complexes. Surprisingly, these components appear unable to interact with each other, or with the EssA protein. We further show that two high molecular weight multimers of EssC detected in whole cells are not dependent upon the presence of EsxA, EsxB or any other Ess component for their assembly.
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Affiliation(s)
- Franziska Jäger
- Divisions of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Martin Zoltner
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Holger Kneuper
- Divisions of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - William N Hunter
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tracy Palmer
- Divisions of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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18
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Eadsforth TC, Pinto A, Luciani R, Tamborini L, Cullia G, De Micheli C, Marinelli L, Cosconati S, Novellino E, Lo Presti L, Cordeiro da Silva A, Conti P, Hunter WN, Costi MP. Characterization of 2,4-Diamino-6-oxo-1,6-dihydropyrimidin-5-yl Ureido Based Inhibitors of Trypanosoma brucei FolD and Testing for Antiparasitic Activity. J Med Chem 2015; 58:7938-48. [PMID: 26322631 PMCID: PMC4621507 DOI: 10.1021/acs.jmedchem.5b00687] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The bifunctional enzyme N5,N10-methylenetetrahydrofolate
dehydrogenase/cyclo
hydrolase (FolD) is essential for growth in Trypanosomatidae. We sought
to develop inhibitors of Trypanosoma brucei FolD
(TbFolD) as potential antiparasitic agents. Compound 2 was synthesized, and the molecular structure was unequivocally
assigned through X-ray crystallography of the intermediate compound 3. Compound 2 showed an IC50 of 2.2
μM, against TbFolD and displayed antiparasitic
activity against T. brucei (IC50 49 μM).
Using compound 2, we were able to obtain the first X-ray
structure of TbFolD in the presence of NADP+ and the inhibitor, which then guided the rational design of a new
series of potent TbFolD inhibitors.
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Affiliation(s)
- Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dow Street, Dundee DD1 5EH, U.K
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli 25, 20133 Milano, Italy
| | - Rosaria Luciani
- Department of Life Science, University of Modena and Reggio Emilia , Via Campi 103, 41125, Modena, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli 25, 20133 Milano, Italy
| | - Gregorio Cullia
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli 25, 20133 Milano, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli 25, 20133 Milano, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli , Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via Montesano 49, 80131 Napoli, Italy
| | - Leonardo Lo Presti
- Dipartimento di Chimica, Università degli Studi di Milano , Via Golgi 19, 20133 Milano, Italy
| | - Anabela Cordeiro da Silva
- Instituto de Investigação e Inovação em Saúde, Instituto de Biologia Molecular e Cellular da Universidade do Porto, Departamento de Ciências Biológicas, Universidade do Porto , Porto, Portugal
| | - Paola Conti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli 25, 20133 Milano, Italy
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dow Street, Dundee DD1 5EH, U.K
| | - Maria P Costi
- Department of Life Science, University of Modena and Reggio Emilia , Via Campi 103, 41125, Modena, Italy
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19
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Baum B, Lecker LSM, Zoltner M, Jaenicke E, Schnell R, Hunter WN, Brenk R. Structures of Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form. Acta Crystallogr F Struct Biol Commun 2015; 71:1020-6. [PMID: 26249693 PMCID: PMC4528935 DOI: 10.1107/s2053230x15010614] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/02/2015] [Indexed: 11/16/2022]
Abstract
Three crystal structures of recombinant P. aeruginosa FabF are reported: the apoenzyme, an active-site mutant and a complex with a fragment of a natural product inhibitor. The characterization provides reagents and new information to support antibacterial drug discovery. Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical means as an antibiotic target in Gram-positive bacteria and represents a potential target in Gram-negative bacteria. The structures of apo FabF, of a C164Q mutant in which the binding site is altered to resemble the substrate-bound state and of a complex with 3-(benzoylamino)-2-hydroxybenzoic acid are reported. This compound mimics aspects of a known natural product inhibitor, platensimycin, and surprisingly was observed binding outside the active site, interacting with a symmetry-related molecule. An unusual feature is a completely buried potassium-binding site that was identified in all three structures. Comparisons suggest that this may represent a conserved structural feature of FabF relevant to fold stability. The new structures provide templates for structure-based ligand design and, together with the protocols and reagents, may underpin a target-based drug-discovery project for urgently needed antibacterials.
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Affiliation(s)
- Bernhard Baum
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, 55128 Mainz, Germany
| | - Laura S M Lecker
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 4EH, Scotland
| | - Martin Zoltner
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 4EH, Scotland
| | - Elmar Jaenicke
- Institut für Molekulare Biophysik, Johannes Gutenberg-Universität, Jakob Welder Weg 26, 55128 Mainz, Germany
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 4EH, Scotland
| | - Ruth Brenk
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, 55128 Mainz, Germany
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20
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Barrack KL, Fyfe PK, Finney AJ, Hunter WN. Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major. Mol Biochem Parasitol 2015; 201:26-30. [PMID: 25982270 PMCID: PMC4539340 DOI: 10.1016/j.molbiopara.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 04/14/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 01/23/2023]
Abstract
Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.
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Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Paul K Fyfe
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alex J Finney
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - William N Hunter
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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21
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Abstract
An introduction to the special issue on molecular parasitology.
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Affiliation(s)
- W N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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22
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Barrack KL, Fyfe PK, Hunter WN. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly. Acta Crystallogr F Struct Biol Commun 2015; 71:539-46. [PMID: 25945706 PMCID: PMC4427162 DOI: 10.1107/s2053230x15000990] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/16/2015] [Indexed: 11/13/2022]
Abstract
The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.
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Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Paul K Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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23
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Hunter WN, Weiss MS. The times they are a-changin' - news from Acta Crystallographica Section F. Acta Crystallogr F Struct Biol Commun 2014; 70:1575. [PMID: 25484202 PMCID: PMC4259216 DOI: 10.1107/s2053230x14024789] [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] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/20/2022]
Abstract
The Editors describe some new developments for Acta Cryst. F.
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Affiliation(s)
- W N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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24
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Khalaf A, Huggan JK, Suckling CJ, Gibson C, Stewart K, Giordani F, Barrett MP, Wong PE, Barrack KL, Hunter WN. Structure-based design and synthesis of antiparasitic pyrrolopyrimidines targeting pteridine reductase 1. J Med Chem 2014; 57:6479-94. [PMID: 25007262 PMCID: PMC4136963 DOI: 10.1021/jm500483b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The treatment of Human African trypanosomiasis remains a major unmet health need in sub-Saharan Africa. Approaches involving new molecular targets are important; pteridine reductase 1 (PTR1), an enzyme that reduces dihydrobiopterin in Trypanosoma spp., has been identified as a candidate target, and it has been shown previously that substituted pyrrolo[2,3-d]pyrimidines are inhibitors of PTR1 from Trypanosoma brucei (J. Med. Chem. 2010, 53, 221-229). In this study, 61 new pyrrolo[2,3-d]pyrimidines have been prepared, designed with input from new crystal structures of 23 of these compounds complexed with PTR1, and evaluated in screens for enzyme inhibitory activity against PTR1 and in vitro antitrypanosomal activity. Eight compounds were sufficiently active in both screens to take forward to in vivo evaluation. Thus, although evidence for trypanocidal activity in a stage I disease model in mice was obtained, the compounds were too toxic to mice for further development.
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Affiliation(s)
- Abedawn
I. Khalaf
- WestCHEM
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Judith K. Huggan
- WestCHEM
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Colin J. Suckling
- WestCHEM
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom, (C.J.S.) E-mail: ; Tel.: +44 141 548 2271
| | - Colin
L. Gibson
- WestCHEM
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Kirsten Stewart
- WestCHEM
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Federica Giordani
- Wellcome
Trust Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation and Glasgow Polyomics, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Michael P. Barrett
- Wellcome
Trust Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation and Glasgow Polyomics, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom,(M.P.B.) E-mail: ; Tel.: +44 141 330 6904
| | - Pui Ee Wong
- Wellcome
Trust Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation and Glasgow Polyomics, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Keri L. Barrack
- Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United
Kingdom
| | - William N. Hunter
- Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United
Kingdom,(W.N.H.) E-mail: ; Tel.: +44 1382 385745
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25
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Kneuper H, Cao ZP, Twomey KB, Zoltner M, Jäger F, Cargill JS, Chalmers J, van der Kooi-Pol MM, van Dijl JM, Ryan RP, Hunter WN, Palmer T. Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylocccus aureus strains. Mol Microbiol 2014; 93:928-43. [PMID: 25040609 PMCID: PMC4285178 DOI: 10.1111/mmi.12707] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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] [Accepted: 07/03/2014] [Indexed: 01/01/2023]
Abstract
The Type VII protein secretion system, found in Gram-positive bacteria, secretes small proteins, containing a conserved W-x-G amino acid sequence motif, to the growth medium. Staphylococcus aureus has a conserved Type VII secretion system, termed Ess, which is dispensable for laboratory growth but required for virulence. In this study we show that there are unexpected differences in the organization of the ess gene cluster between closely related strains of S. aureus. We further show that in laboratory growth medium different strains of S. aureus secrete the EsxA and EsxC substrate proteins at different growth points, and that the Ess system in strain Newman is inactive under these conditions. Systematic deletion analysis in S. aureus RN6390 is consistent with the EsaA, EsaB, EssA, EssB, EssC and EsxA proteins comprising core components of the secretion machinery in this strain. Finally we demonstrate that the Ess secretion machinery of two S. aureus strains, RN6390 and COL, is important for nasal colonization and virulence in the murine lung pneumonia model. Surprisingly, however, the secretion system plays no role in the virulence of strain SA113 under the same conditions.
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Affiliation(s)
- Holger Kneuper
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK
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26
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Rimsa V, Eadsforth TC, Joosten RP, Hunter WN. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies. ACTA ACUST UNITED AC 2014; 70:279-89. [PMID: 24531462 PMCID: PMC3940198 DOI: 10.1107/s1399004713026801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 03/15/2013] [Accepted: 09/30/2013] [Indexed: 01/01/2023]
Abstract
The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.
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Affiliation(s)
- Vadim Rimsa
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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27
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Rimsa V, Eadsforth TC, Hunter WN. Two high-resolution structures of the human E3 ubiquitin ligase Siah1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1339-43. [PMID: 24316825 PMCID: PMC3855715 DOI: 10.1107/s1744309113031448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 10/08/2013] [Accepted: 11/18/2013] [Indexed: 01/07/2023]
Abstract
Siah1 is an E3 ubiquitin ligase that contributes to proteasome-mediated degradation of multiple targets in key cellular processes and which shows promise as a therapeutic target in oncology. Structures of a truncated Siah1 bound to peptide-based inhibitors have been reported. Here, new crystallization conditions have allowed the determination of a construct encompassing dual zinc-finger subdomains and substrate-binding domains at significantly higher resolution. Although the crystals appear isomorphous, two structures present distinct states in which the spatial orientation of one zinc-finger subdomain differs with respect to the rest of the dimeric protein. Such a difference, which is indicative of conformational freedom, infers potential biological relevance related to recognition of binding partners. The crystallization conditions and improved models of Siah1 may aid future studies investigating Siah1-ligand complexes.
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Affiliation(s)
- Vadim Rimsa
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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28
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Srikannathasan V, English G, Bui NK, Trunk K, O'Rourke PEF, Rao VA, Vollmer W, Coulthurst SJ, Hunter WN. Structural basis for type VI secreted peptidoglycan DL-endopeptidase function, specificity and neutralization in Serratia marcescens. Acta Crystallogr D Biol Crystallogr 2013; 69:2468-82. [PMID: 24311588 PMCID: PMC3852654 DOI: 10.1107/s0907444913022725] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/13/2013] [Indexed: 11/10/2022]
Abstract
Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endopeptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between γ-D-glutamic acid and L-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muropeptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure-activity relationships of Ssp1 and, by comparison, of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1-Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2-Rap2a orthologues suggest that the specificity of these immunity proteins for neutralizing effectors is fold-dependent and that in cases where the fold is conserved sequence differences contribute to the specificity of effector-immunity protein interactions.
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Affiliation(s)
- Velupillai Srikannathasan
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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29
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Dawson A, Trumper P, Chrysostomou G, Hunter WN. Structure of diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase from Acinetobacter baumannii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:611-7. [PMID: 23722836 PMCID: PMC3668577 DOI: 10.1107/s174430911301292x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 03/18/2013] [Accepted: 05/11/2013] [Indexed: 11/11/2022]
Abstract
The structure of a bifunctional deaminase/reductase involved in riboflavin biosynthesis in the pathogen A. baumannii has been determined in two crystal forms. The bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase (RibD) represents a potential antibacterial drug target. The structure of recombinant Acinetobacter baumannii RibD is reported in orthorhombic and tetragonal crystal forms at 2.2 and 2.0 Å resolution, respectively. Comparisons with orthologous structures in the Protein Data Bank indicated close similarities. The tetragonal crystal form was obtained in the presence of guanosine monophosphate, which surprisingly was observed to occupy the adenine-binding site of the reductase domain.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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30
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Fleming JR, Morgan RE, Fyfe PK, Kelly SM, Hunter WN. The architecture of Trypanosoma brucei tubulin-binding cofactor B and implications for function. FEBS J 2013; 280:3270-80. [PMID: 23627368 PMCID: PMC3806363 DOI: 10.1111/febs.12308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 02/04/2013] [Revised: 04/01/2013] [Accepted: 04/23/2013] [Indexed: 01/01/2023]
Abstract
Tubulin-binding cofactor (TBC)-B is implicated in the presentation of α-tubulin ready to polymerize, and at the correct levels to form microtubules. Bioinformatics analyses, including secondary structure prediction, CD, and crystallography, were combined to characterize the molecular architecture of Trypanosoma brucei TBC-B. An efficient recombinant expression system was prepared, material-purified, and characterized by CD. Extensive crystallization screening, allied with the use of limited proteolysis, led to structures of the N-terminal ubiquitin-like and C-terminal cytoskeleton-associated protein with glycine-rich segment domains at 2.35-Å and 1.6-Å resolution, respectively. These are compact globular domains that appear to be linked by a flexible segment. The ubiquitin-like domain contains two lysines that are spatially conserved with residues known to participate in ubiquitinylation, and so may represent a module that, through covalent attachment, regulates the signalling and/or protein degradation associated with the control of microtubule assembly, catastrophe, or function. The TBC-B C-terminal cytoskeleton-associated protein with glycine-rich segment domain, a known tubulin-binding structure, is the only such domain encoded by the T. brucei genome. Interestingly, in the crystal structure, the peptide-binding groove of this domain forms intermolecular contacts with the C-terminus of a symmetry-related molecule, an association that may mimic interactions with the C-terminus of α-tubulin or other physiologically relevant partners. The interaction of TBC-B with the α-tubulin C-terminus may, in particular, protect from post-translational modifications, or simply assist in the shepherding of the protein into polymerization.
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Affiliation(s)
- Jennifer R Fleming
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
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31
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Rao VA, Shepherd SM, Owen R, Hunter WN. Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:243-7. [PMID: 23519796 PMCID: PMC3606566 DOI: 10.1107/s1744309113002352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/23/2013] [Indexed: 05/29/2023]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) represents a potential antimicrobial drug target. The crystal structure of recombinant Pseudomonas aeruginosa IMPDH has been determined to a resolution of 2.25 Å. The structure is a homotetramer of subunits dominated by a (β/α)8-barrel fold, consistent with other known structures of IMPDH. Also in common with previous work, the cystathionine β-synthase domains, residues 92-204, are not present in the model owing to disorder. However, unlike the majority of available structures, clearly defined electron density exists for a loop that creates part of the active site. This loop, composed of residues 297-315, links α8 and β9 and carries the catalytic Cys304. P. aeruginosa IMPDH shares a high level of sequence identity with bacterial and protozoan homologues, with residues involved in binding substrate and the NAD+ cofactor being conserved. Specific differences that have been proven to contribute to selectivity against the human enzyme in a study of Cryptosporidium parvum IMPDH are also conserved, highlighting the potential value of IMPDH as a drug target.
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Affiliation(s)
- Vincenzo A. Rao
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Sharon M. Shepherd
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Richard Owen
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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32
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Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G. The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:25-34. [PMID: 23295481 PMCID: PMC3539698 DOI: 10.1107/s1744309112044739] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 09/13/2012] [Accepted: 10/29/2012] [Indexed: 12/25/2022]
Abstract
Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.
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Affiliation(s)
- Lucille Moynie
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Tatyana Sandalova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | | | - Jason W. Schmidberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Magnus Alphey
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Cyprian Cukier
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Fraser Duthie
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Jolanta Kopec
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Agata Jacewicz
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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33
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Eadsforth TC, Maluf FV, Hunter WN. Acinetobacter baumannii FolD ligand complexes --potent inhibitors of folate metabolism and a re-evaluation of the structure of LY374571. FEBS J 2012; 279:4350-60. [PMID: 23050773 DOI: 10.1111/febs.12025] [Citation(s) in RCA: 13] [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] [Received: 08/09/2012] [Revised: 09/07/2012] [Accepted: 10/04/2012] [Indexed: 01/26/2023]
Abstract
The bifunctional N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram-negative pathogen Acinetobacter baumanni and determined high-resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed.
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Affiliation(s)
- Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
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34
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English G, Trunk K, Rao VA, Srikannathasan V, Hunter WN, Coulthurst SJ. New secreted toxins and immunity proteins encoded within the Type VI secretion system gene cluster of Serratia marcescens. Mol Microbiol 2012; 86:921-36. [PMID: 22957938 PMCID: PMC3533786 DOI: 10.1111/mmi.12028] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [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] [Accepted: 09/03/2012] [Indexed: 12/29/2022]
Abstract
Protein secretion systems are critical to bacterial virulence and interactions with other organisms. The Type VI secretion system (T6SS) is found in many bacterial species and is used to target either eukaryotic cells or competitor bacteria. However, T6SS-secreted proteins have proven surprisingly elusive. Here, we identified two secreted substrates of the antibacterial T6SS from the opportunistic human pathogen, Serratia marcescens. Ssp1 and Ssp2, both encoded within the T6SS gene cluster, were confirmed as antibacterial toxins delivered by the T6SS. Four related proteins encoded around the Ssp proteins (‘Rap’ proteins) included two specifically conferring self-resistance (‘immunity’) against T6SS-dependent Ssp1 or Ssp2 toxicity. Biochemical characterization revealed specific, tight binding between cognate Ssp–Rap pairs, forming complexes of 2:2 stoichiometry. The atomic structures of two Rap proteins were solved, revealing a novel helical fold, dependent on a structural disulphide bond, a structural feature consistent with their functional localization. Homologues of the Serratia Ssp and Rap proteins are found encoded together within other T6SS gene clusters, thus they represent founder members of new families of T6SS-secreted and cognate immunity proteins. We suggest that Ssp proteins are the original substrates of the S. marcescens T6SS, before horizontal acquisition of other T6SS-secreted toxins. Molecular insight has been provided into how pathogens utilize antibacterial T6SSs to overcome competitors and succeed in polymicrobial niches.
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Affiliation(s)
- Grant English
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK
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Fyfe PK, Westrop GD, Ramos T, Müller S, Coombs GH, Hunter WN. Structure of Leishmania major cysteine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:738-43. [PMID: 22750854 PMCID: PMC3388911 DOI: 10.1107/s1744309112019124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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: 02/20/2012] [Accepted: 04/28/2012] [Indexed: 01/19/2023]
Abstract
A crystallographic and biochemical study of L. major cysteine synthase, which is a pyridoxyl phosphate-dependent enzyme, is reported. The structure was determined to 1.8 Å resolution and revealed that the cofactor has been lost and that a fragment of γ-poly-d-glutamic acid, a crystallization ingredient, was bound in the active site. The enzyme was inhibited by peptides. Cysteine biosynthesis is a potential target for drug development against parasitic Leishmania species; these protozoa are responsible for a range of serious diseases. To improve understanding of this aspect of Leishmania biology, a crystallographic and biochemical study of L. major cysteine synthase has been undertaken, seeking to understand its structure, enzyme activity and modes of inhibition. Active enzyme was purified, assayed and crystallized in an orthorhombic form with a dimer in the asymmetric unit. Diffraction data extending to 1.8 Å resolution were measured and the structure was solved by molecular replacement. A fragment of γ-poly-d-glutamic acid, a constituent of the crystallization mixture, was bound in the enzyme active site. Although a d-glutamate tetrapeptide had insignificant inhibitory activity, the enzyme was competitively inhibited (Ki = 4 µM) by DYVI, a peptide based on the C-terminus of the partner serine acetyltransferase with which the enzyme forms a complex. The structure surprisingly revealed that the cofactor pyridoxal phosphate had been lost during crystallization.
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Affiliation(s)
- Paul K Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Tidten-Luksch N, Grimaldi R, Torrie LS, Frearson JA, Hunter WN, Brenk R. IspE inhibitors identified by a combination of in silico and in vitro high-throughput screening. PLoS One 2012; 7:e35792. [PMID: 22563402 PMCID: PMC3340893 DOI: 10.1371/journal.pone.0035792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/22/2012] [Indexed: 11/19/2022] Open
Abstract
CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens.
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Affiliation(s)
| | | | | | | | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (WNH); (RB)
| | - Ruth Brenk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (WNH); (RB)
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Abstract
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The twin-arginine translocation (Tat) pathway is a protein
targeting system found in bacteria, archaea, and chloroplasts. Proteins
are directed to the Tat translocase by N-terminal signal peptides
containing SRRxFLK “twin-arginine” amino acid motifs.
The key feature of the Tat system is its ability to transport fully
folded proteins across ionically sealed membranes. For this reason
the Tat pathway has evolved for the assembly of extracytoplasmic redox
enzymes that must bind cofactors, and so fold, prior to export. It
is important that only cofactor-loaded, folded precursors are presented
for export, and cellular processes have been unearthed that regulate
signal peptide activity. One mechanism, termed “Tat proofreading”,
involves specific signal peptide binding proteins or chaperones. The
archetypal Tat proofreading chaperones belong to the TorD family,
which are dedicatedto the assembly of molybdenum-dependent redox
enzymes in bacteria. Here, a gene cluster was identified in the archaeon Archaeoglobus fulgidusthat is predicted to encode a putative
molybdenum-dependent tetrathionate reductase. The gene cluster also
encodes a TorD family chaperone (AF0160 or TtrD) and in this work
TtrD is shown to bind specifically to the Tat signal peptide of the
TtrA subunit of the tetrathionate reductase. In addition, the 3D crystal
structure of TtrD is presented at 1.35 Å resolution and a nine-residue
binding epitope for TtrD is identified within the TtrA signal peptide
close to the twin-arginine targeting motif. This work suggests that
archaea may employ a chaperone-dependent Tat proofreading system that
is similar to that utilized by bacteria.
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Affiliation(s)
- Sarah J Coulthurst
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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Hunter WN. Isoprenoid precursor biosynthesis offers potential targets for drug discovery against diseases caused by apicomplexan parasites. Curr Top Med Chem 2011; 11:2048-59. [PMID: 21619509 DOI: 10.2174/156802611796575867] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 07/27/2010] [Indexed: 02/08/2023]
Abstract
Two, simple, C5 compounds, dimethylally diphosphate and isopentenyl diphosphate, are the universal precursors of isoprenoids, a large family of natural products involved in numerous important biological processes. Two distinct biosynthetic pathways have evolved to supply these precursors. Humans use the mevalonate route whilst many species of bacteria including important pathogens, plant chloroplasts and apicomplexan parasites exploit the non-mevalonate pathway. The absence from humans, combined with genetic and chemical validation suggests that the non-mevalonate pathway holds the potential to support new drug discovery programmes targeting Gram-negative bacteria and the apicomplexan parasites responsible for causing serious human diseases, and also infections of veterinary importance. The non-mevalonate pathway relies on eight enzyme-catalyzed stages exploiting a range of cofactors and metal ions. A wealth of structural and mechanistic data, mainly derived from studies of bacterial enzymes, now exists for most components of the pathway and these will be described. Particular attention will be paid to how these data inform on the apicomplexan orthologues concentrating on the enzymes from Plasmodium spp. these cause malaria, one the most important parasitic diseases in the world today.
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Affiliation(s)
- William N Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, UK.
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Barakate A, Stephens J, Goldie A, Hunter WN, Marshall D, Hancock RD, Lapierre C, Morreel K, Boerjan W, Halpin C. Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco. Plant Cell 2011; 23:4492-506. [PMID: 22158465 PMCID: PMC3269879 DOI: 10.1105/tpc.111.089037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 07/27/2011] [Accepted: 11/16/2011] [Indexed: 05/02/2023]
Abstract
The manipulation of lignin could, in principle, facilitate efficient biofuel production from plant biomass. Despite intensive study of the lignin pathway, uncertainty exists about the enzyme catalyzing the last step in syringyl (S) monolignol biosynthesis, the reduction of sinapaldehyde to sinapyl alcohol. Traditional schemes of the pathway suggested that both guaiacyl (G) and S monolignols are produced by a single substrate-versatile enzyme, cinnamyl alcohol dehydrogenase (CAD). This was challenged by the discovery of a novel sinapyl alcohol dehydrogenase (SAD) that preferentially uses sinapaldehyde as a substrate and that was claimed to regulate S lignin biosynthesis in angiosperms. Consequently, most pathway schemes now show SAD (or SAD and CAD) at the sinapaldehyde reduction step, although functional evidence is lacking. We cloned SAD from tobacco (Nicotiana tabacum) and suppressed it in transgenic plants using RNA interference-inducing vectors. Characterization of lignin in the woody stems shows no change to content, composition, or structure, and S lignin is normal. By contrast, plants additionally suppressed in CAD have changes to lignin structure and S:G ratio and have increased sinapaldehyde in lignin, similar to plants suppressed in CAD alone. These data demonstrate that CAD, not SAD, is the enzyme responsible for S lignin biosynthesis in woody angiosperm xylem.
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Affiliation(s)
- Abdellah Barakate
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Jennifer Stephens
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Alison Goldie
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David Marshall
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | | | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique-AgroParisTech, Unité Mixte de Recherche 1318, 78026 Versailles, France
| | - Kris Morreel
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B–9052 Ghent, Belgium
- Department of Plant Biotechnology, Ghent University, B–9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, B–9052 Ghent, Belgium
- Department of Plant Biotechnology, Ghent University, B–9052 Ghent, Belgium
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
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Rao VA, Shepherd SM, English G, Coulthurst SJ, Hunter WN. The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system. Acta Crystallogr D Biol Crystallogr 2011; 67:1065-72. [PMID: 22120744 PMCID: PMC3225178 DOI: 10.1107/s0907444911046300] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 11/02/2011] [Indexed: 11/28/2022]
Abstract
The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.
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Affiliation(s)
- Vincenzo A Rao
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Eadsforth TC, Cameron S, Hunter WN. The crystal structure of Leishmania major N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase and assessment of a potential drug target. Mol Biochem Parasitol 2011; 181:178-85. [PMID: 22108435 PMCID: PMC3368264 DOI: 10.1016/j.molbiopara.2011.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 01/24/2023]
Abstract
Three enzyme activities in the protozoan Leishmania major, namely N5,N10-methylenetetrahydrofolate dehydrogenase/N5,N10-methenyltetrahydrofolate cyclohydrolase (DHCH) and N10-formyltetrahydrofolate ligase (FTL) produce the essential intermediate N10-formyltetrahydrofolate. Although trypanosomatids possess at least one functional DHCH, the same is not true for FTL, which is absent in Trypanosoma brucei. Here, we present the 2.7 Å resolution crystal structure of the bifunctional apo-DHCH from L. major, which is a potential drug target. Sequence alignments show that the cytosolic enzymes found in trypanosomatids share a high level of identity of approximately 60%. Additionally, residues that interact and participate in catalysis in the human homologue are conserved amongst trypanosomatid sequences and this may complicate attempts to derive potent, parasite specific DHCH inhibitors.
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O'Rourke PEF, Eadsforth TC, Fyfe PK, Shepherd SM, Hunter WN. Pseudomonas aeruginosa 4-amino-4-deoxychorismate lyase: spatial conservation of an active site tyrosine and classification of two types of enzyme. PLoS One 2011; 6:e24158. [PMID: 21935381 PMCID: PMC3174152 DOI: 10.1371/journal.pone.0024158] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/01/2011] [Indexed: 01/17/2023] Open
Abstract
4-Amino-4-deoxychorismate lyase (PabC) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. This is an essential activity for the growth of gram-negative bacteria, including important pathogens such as Pseudomonas aeruginosa. A high-resolution (1.75 Å) crystal structure of PabC from P. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. Residues around the pyridoxal 5'-phosphate cofactor are highly conserved adding support to aspects of a mechanism generic for enzymes carrying that cofactor. However, we suggest that PabC can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly. We considered that the conserved tyrosine might indicate a direct role in catalysis: that of providing a proton to reduce the olefin moiety of substrate as pyruvate is released. A threonine had previously been suggested to fulfill such a role prior to our observation of the structurally conserved tyrosine. We have been unable to elucidate an experimentally determined structure of PabC in complex with ligands to inform on mechanism and substrate specificity. Therefore we constructed a computational model of the catalytic intermediate docked into the enzyme active site. The model suggests that the conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate. However, this residue does not appear to participate in interactions with the C atom that undergoes an sp(2) to sp(3) conversion as pyruvate is produced. The model and our comparisons rather support the hypothesis that an active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism.
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Affiliation(s)
- Patrick E. F. O'Rourke
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul K. Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sharon M. Shepherd
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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Morgan RE, Batot GO, Dement JM, Rao VA, Eadsforth TC, Hunter WN. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate. BMC Struct Biol 2011; 11:21. [PMID: 21554707 PMCID: PMC3098144 DOI: 10.1186/1472-6807-11-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/09/2011] [Indexed: 11/22/2022]
Abstract
Background The enzyme dihydropteroate synthase (DHPS) participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. Results An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS) was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Conclusion Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence identity. The presence of 7,8-dihydropteroate in the binding site provides details about ligand recognition by the enzyme and the different states of the enzyme allow us to visualize distinct conformational states of loops adjacent to the active site. Improved drugs to combat infections by Burkholderia sp. and related Gram-negative bacteria are sought and our study now provides templates to assist that process and allow us to discuss new ways of inhibiting DHPS.
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Affiliation(s)
- Rachel E Morgan
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
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Dawson A, Fyfe PK, Gillet F, Hunter WN. Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity. BMC Struct Biol 2011; 11:19. [PMID: 21513522 PMCID: PMC3097144 DOI: 10.1186/1472-6807-11-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/22/2011] [Indexed: 11/23/2022]
Abstract
Background MenH (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase) is a key enzyme in the biosynthesis of menaquinone, catalyzing an unusual 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate. Results The crystal structure of Staphylococcus aureus MenH has been determined at 2 Å resolution. In the absence of a complex to inform on aspects of specificity a model of the enzyme-substrate complex has been used in conjunction with previously published kinetic analyses, site-directed mutagenesis studies and comparisons with orthologues to investigate the structure and reactivity of MenH. Conclusions The overall basic active site displays pronounced hydrophobic character on one side and these properties complement those of the substrate. A complex network of hydrogen bonds involving well-ordered water molecules serves to position key residues participating in the recognition of substrate and subsequent catalysis. We propose a proton shuttle mechanism, reliant on a catalytic triad consisting of Ser89, Asp216 and His243. The reaction is initiated by proton abstraction from the substrate by an activated Ser89. The propensity to form a conjugated system provides the driving force for pyruvate elimination. During the elimination, a methylene group is converted to a methyl and we judge it likely that His243 provides a proton, previously acquired from Ser89 for that reduction. A conformational change of the protonated His243 may be encouraged by the presence of an anionic intermediate in the active site.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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Rimsa V, Eadsforth T, Hunter WN. The role of Co²+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:442-5. [PMID: 21505236 DOI: 10.1107/s1744309111005835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 02/16/2011] [Indexed: 11/10/2022]
Abstract
Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium-resolution electron-density map of the catalytic domain of human sentrin-specific protease 1 (SENP1), a strong feature indicative of an ordered divalent cation was noted. This was assigned as Co(2+), an essential component of the crystallization mixture. The ion displays tetrahedral coordination by Glu430 and His640 from one molecule and the corresponding residues from a symmetry-related molecule. Analysis of the data derived from a previous structure of SENP1 suggested that Co(2+) had been overlooked and re-refinement supported this conclusion. High-throughput automated re-refinement protocols also failed to mark the Co(2+) position, supporting the requirement for the incorporation of as much information as possible to enhance the value of such protocols.
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Affiliation(s)
- Vadim Rimsa
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Barrack KL, Tulloch LB, Burke LA, Fyfe PK, Hunter WN. Structure of recombinant Leishmania donovani pteridine reductase reveals a disordered active site. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 67:33-7. [PMID: 21206018 PMCID: PMC3079966 DOI: 10.1107/s174430911004724x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [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: 09/12/2010] [Accepted: 11/15/2010] [Indexed: 02/04/2023]
Abstract
The structure of L. donovani pteridine reductase has been targeted to assist in a program of structure-based inhibitor research. Crystals that diffracted to 2.5 Å resolution were obtained and the structure has been solved. Unfortunately, the active site is disordered and this crystal form is unsuitable for use in characterizing enzyme–ligand interactions. Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species, protozoa that are responsible for a range of serious diseases found in tropical and subtropical parts of the world. As part of a structure-based approach to inhibitor development, specifically targeting Leishmania species, well ordered crystals of L. donovani PTR1 were sought to support the characterization of complexes formed with inhibitors. An efficient system for recombinant protein production was prepared and the enzyme was purified and crystallized in an orthorhombic form with ammonium sulfate as the precipitant. Diffraction data were measured to 2.5 Å resolution and the structure was solved by molecular replacement. However, a sulfate occupies a phosphate-binding site used by NADPH and occludes cofactor binding. The nicotinamide moiety is a critical component of the active site and without it this part of the structure is disordered. The crystal form obtained under these conditions is therefore unsuitable for the characterization of inhibitor complexes.
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Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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47
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Dawson A, Tulloch LB, Barrack KL, Hunter WN. High-resolution structures of Trypanosoma brucei pteridine reductase ligand complexes inform on the placement of new molecular entities in the active site of a potential drug target. Acta Crystallogr D Biol Crystallogr 2010; 66:1334-40. [PMID: 21123874 PMCID: PMC3655514 DOI: 10.1107/s0907444910040886] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/12/2010] [Indexed: 03/07/2023]
Abstract
Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species. These protozoa cause serious diseases for which current therapies are inadequate. High-resolution structures have been determined, using data between 1.6 and 1.1 Å resolution, of T. brucei PTR1 in complex with pemetrexed, trimetrexate, cyromazine and a 2,4-diaminopyrimidine derivative. The structures provide insight into the interactions formed by new molecular entities in the enzyme active site with ligands that represent lead compounds for structure-based inhibitor development and to support early-stage drug discovery.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | | | - Keri L. Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Sainsbury S, Bird L, Rao V, Shepherd SM, Stuart DI, Hunter WN, Owens RJ, Ren J. Crystal structures of penicillin-binding protein 3 from Pseudomonas aeruginosa: comparison of native and antibiotic-bound forms. J Mol Biol 2010; 405:173-84. [PMID: 20974151 PMCID: PMC3025346 DOI: 10.1016/j.jmb.2010.10.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/08/2010] [Accepted: 10/15/2010] [Indexed: 11/24/2022]
Abstract
We report the first crystal structures of a penicillin-binding protein (PBP), PBP3, from Pseudomonas aeruginosa in native form and covalently linked to two important β-lactam antibiotics, carbenicillin and ceftazidime. Overall, the structures of apo and acyl complexes are very similar; however, variations in the orientation of the amino-terminal membrane-proximal domain relative to that of the carboxy-terminal transpeptidase domain indicate interdomain flexibility. Binding of either carbenicillin or ceftazidime to purified PBP3 increases the thermostability of the enzyme significantly and is associated with local conformational changes, which lead to a narrowing of the substrate-binding cleft. The orientations of the two β-lactams in the active site and the key interactions formed between the ligands and PBP3 are similar despite differences in the two drugs, indicating a degree of flexibility in the binding site. The conserved binding mode of β-lactam-based inhibitors appears to extend to other PBPs, as suggested by a comparison of the PBP3/ceftazidime complex and the Escherichia coli PBP1b/ceftoxamine complex. Since P. aeruginosa is an important human pathogen, the structural data reveal the mode of action of the frontline antibiotic ceftazidime at the molecular level. Improved drugs to combat infections by P. aeruginosa and related Gram-negative bacteria are sought and our study provides templates to assist that process and allows us to discuss new ways of inhibiting PBPs.
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Affiliation(s)
- Sarah Sainsbury
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Louise Bird
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Oxfordshire OX11 0FA, UK
| | - Vincenzo Rao
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sharon M. Shepherd
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David I. Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - William N. Hunter
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Raymond J. Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Oxfordshire OX11 0FA, UK
- Corresponding authors. R. J. Owens is to be contacted at: Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Jingshan Ren
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Corresponding authors. R. J. Owens is to be contacted at: Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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Fleming JR, Dawson A, Hunter WN. Crystal structure of Leishmania major ADP-ribosylation factor-like 1 and a classification of related GTPase family members in this Kinetoplastid. Mol Biochem Parasitol 2010; 174:141-4. [PMID: 20801163 DOI: 10.1016/j.molbiopara.2010.08.002] [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: 03/08/2010] [Revised: 08/11/2010] [Accepted: 08/13/2010] [Indexed: 12/24/2022]
Abstract
ADP-ribosylation factor-like (ARL) proteins are small GTPases that undergo conformational changes upon nucleotide binding, and which regulate the affinity of ARLs for binding other proteins, lipids or membranes. There is a paucity of structural data on this family of proteins in the Kinetoplastida, despite studies implicating them in key events related to vesicular transport and regulation of microtubule-dependent processes. The crystal structure of Leishmania major ARL1 in complex with GDP has been determined to 2.1 Å resolution and reveals a high degree of structural conservation with human ADP-ribosylation factor 1 (ARF1). Putative L. major and Trypanosoma brucei ARF/ARL family members have been classified based on structural considerations, amino acid sequence conservation combined with functional data on Kinetoplastid and human orthologues. This classification may guide future studies designed to elucidate the function of specific family members.
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Affiliation(s)
- Jennifer R Fleming
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
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50
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Fyfe PK, Dawson A, Hutchison MT, Cameron S, Hunter WN. Structure of Staphylococcus aureus adenylosuccinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery. Acta Crystallogr D Biol Crystallogr 2010; 66:881-8. [PMID: 20693687 PMCID: PMC2917274 DOI: 10.1107/s0907444910020081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 05/27/2010] [Indexed: 12/03/2022]
Abstract
The 2.5 Å resolution structure of S. aureus adenylosuccinate lyase is reported and compared with those of orthologues to assess its potential as a template for early stage drug discovery. AMP and a putative assignment of oxalate, the latter an artefact possibly arising from an impurity in the PEG used for crystallization, occupy the active site. The medium-resolution structure of adenylosuccinate lyase (PurB) from the bacterial pathogen Staphylococcus aureus in complex with AMP is presented. Oxalate, which is likely to be an artifact of crystallization, has been modelled in the active site and occupies a position close to that where succinate is observed in orthologous structures. PurB catalyzes reactions that support the provision of purines and the control of AMP/fumarate levels. As such, the enzyme is predicted to be essential for the survival of S. aureus and to be a potential therapeutic target. Comparisons of this pathogen PurB with the enzyme from Escherichia coli are presented to allow discussion concerning the enzyme mechanism. Comparisons with human PurB suggest that the close similarity of the active sites would make it difficult to identify species-specific inhibitors for this enyme. However, there are differences in the way that the subunits are assembled into dimers. The distinct subunit–subunit interfaces may provide a potential area to target by exploiting the observation that creation of the enzyme active site is dependent on oligomerization.
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Affiliation(s)
- Paul K Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD15EH, Scotland
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