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Gilkes JM, Frampton RA, Board AJ, Hudson AO, Price TG, Morris VK, Crittenden DL, Muscroft‐Taylor AC, Sheen CR, Smith GR, Dobson RCJ. A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction. Protein Sci 2024; 33:e5083. [PMID: 38924211 PMCID: PMC11201819 DOI: 10.1002/pro.5083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/16/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid-a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
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Affiliation(s)
- Jenna M. Gilkes
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Rebekah A. Frampton
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Amanda J. Board
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life SciencesRochesterNew YorkUSA
| | - Thomas G. Price
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | - Vanessa K. Morris
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Deborah L. Crittenden
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | | | - Campbell R. Sheen
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
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2
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Christoff RM, Al Bayer M, Soares da Costa TP, Perugini MA, Abbott BM. Enhancing allosteric inhibition of dihydrodipicolinate synthase through the design and synthesis of novel dimeric compounds. RSC Med Chem 2023; 14:1698-1703. [PMID: 37731698 PMCID: PMC10507794 DOI: 10.1039/d3md00044c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/01/2023] [Indexed: 09/22/2023] Open
Abstract
The synthesis of the first dimeric inhibitor of E. coli dihydrodipicolinate synthase (DHDPS) is reported herein. Inspired by 2,4-thiazolidinedione based ligands previously shown to inhibit DHDPS, a series of dimeric inhibitors were designed and synthesised, incorporating various alkyl chain bridges between two 2,4-thiazolidinedione moieties. Aiming to exploit the multimeric nature of this enzyme and enhance potency, a dimeric compound with a single methylene bridge achieved the desired outcome with low micromolar inhibition of E. coli DHDPS observed. This work highlights the continued importance of investigation into DHDPS as an antibacterial target. Furthermore, we demonstrate the design of dimeric ligands can provide a promising strategy to improve potency in the search for novel bioactive compounds.
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Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Mohammad Al Bayer
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
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3
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Mitsakos V. Colorimetric ortho-aminobenzaldehyde assay developed for the high-throughput chemical screening of inhibitors against dihydrodipicolinate synthase from pathogenic bacteria. Heliyon 2023; 9:e14304. [PMID: 36967940 PMCID: PMC10036502 DOI: 10.1016/j.heliyon.2023.e14304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
In search of a new class of antibacterial agents, compounds that target the essential bacterial enzyme, dihydrodipicolinate synthase (DHDPS), are of interest to drug discovery efforts. DHDPS catalyzes the first committed step in the diaminopimelate (DAP) pathway to the biosynthesis of lysine in bacteria and plants. The ortho-aminobenzaldehyde (o-ABA) assay is typically used as a qualitative tool for identifying fractions containing DHDPS during purification. This report is about the development of a high-throughput o-ABA assay format for the quantification of DHDPS enzyme activity using multi-well plates. The colorimetric assay is suitable for determining enzymatic parameters (K M and Vmax) and identifying inhibitors of DHDPS in a high-throughput screen.
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4
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Ugalde CL, Gordon SE, Shambrook M, Nasiri Kenari A, Coleman BM, Perugini MA, Lawson VA, Finkelstein DI, Hill AF. An intact membrane is essential for small extracellular vesicle-induced modulation of α-synuclein fibrillization. J Extracell Vesicles 2020; 10:e12034. [PMID: 33318779 PMCID: PMC7726797 DOI: 10.1002/jev2.12034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/09/2020] [Accepted: 11/08/2020] [Indexed: 01/05/2023] Open
Abstract
The misfolding and fibrillization of the protein, α-synuclein (αsyn), is associated with neurodegenerative disorders referred to as the synucleinopathies. Understanding the mechanisms of αsyn misfolding is an important area of interest given that αsyn misfolding contributes to disease pathogenesis. While many studies report the ability of synthetic lipid membranes to modulate αsyn folding, there is little data pertaining to the mechanism(s) of this interaction. αSyn has previously been shown to associate with small lipid vesicles released by cells called extracellular vesicles (EVs) and it is postulated these interactions may assist in the spreading of pathological forms of this protein. Together, this presents the need for robust characterisation studies on αsyn fibrillization using biologically-derived vesicles. In this study, we comprehensively characterised the ability of lipid-rich small extracellular vesicles (sEVs) to alter the misfolding of αsyn induced using the Protein Misfolding Cyclic Amplification (PMCA) assay. The biochemical and biophysical properties of misfolded αsyn were examined using a range of techniques including: Thioflavin T fluorescence, transmission electron microscopy, analytical centrifugation and western immunoblot coupled with protease resistance assays and soluble/insoluble fractionation. We show that sEVs cause an acceleration in αsyn fibrillization and provide comprehensive evidence that this results in an increase in the abundance of mature insoluble fibrillar species. In order to elucidate the relevance of the lipid membrane to this interaction, sEV lipid membranes were modified by treatment with methanol, or a combination of methanol and sarkosyl. These treatments altered the ultrastructure of the sEVs without changing the protein cargo. Critically, these modified sEVs had a reduced ability to influence αsyn fibrillization compared to untreated counterparts. This study reports the first comprehensive examination of αsyn:EV interactions and demonstrates that sEVs are powerful modulators of αsyn fibrillization, which is mediated by the sEV membrane. In doing so, this work provides strong evidence for a role of sEVs in contributing directly to αsyn misfolding in the synucleinopathy disorders.
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Affiliation(s)
- Cathryn L. Ugalde
- La Trobe Institute of Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
- Howard Florey Institute of Neuroscience and Mental HealthParkvilleVictoriaAustralia
- Department of Microbiology and ImmunologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Shane E. Gordon
- La Trobe Institute of Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Mitch Shambrook
- La Trobe Institute of Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | | | - Bradley M. Coleman
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Matthew A. Perugini
- La Trobe Institute of Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Victoria A. Lawson
- Department of Microbiology and ImmunologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - David I. Finkelstein
- Howard Florey Institute of Neuroscience and Mental HealthParkvilleVictoriaAustralia
| | - Andrew F. Hill
- La Trobe Institute of Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
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5
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Crowther JM, Broadhurst M, Laue TM, Jameson GB, Hodgkinson AJ, Dobson RCJ. On the utility of fluorescence-detection analytical ultracentrifugation in probing biomolecular interactions in complex solutions: a case study in milk. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:677-685. [PMID: 33052462 DOI: 10.1007/s00249-020-01468-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/24/2022]
Abstract
β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Using the fluorescence-detection system within the analytical ultracentrifuge, we observed an interaction involving fluorescently labelled β-lactoglobulin in its native environment, i.e. cow and goat milk, for the first time. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. The identification of these interactions, made possible through the use of fluorescence-detected analytical ultracentrifugation, provides possible clues to the long debated physiological function of this abundant milk protein.
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Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
| | - Marita Broadhurst
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Thomas M Laue
- Center To Advance Molecular Interaction Science, University of New Hampshire, Durham, NH, USA
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand.
- On-Farm R&D, Farm Source, Fonterra Co-Operative Group, Hamilton, 3200, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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6
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Schmitz RA, Dietl A, Müller M, Berben T, Op den Camp HJM, Barends TRM. Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway. Acta Crystallogr F Struct Biol Commun 2020; 76:199-208. [PMID: 32356521 PMCID: PMC7193512 DOI: 10.1107/s2053230x20005294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and L-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.
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Affiliation(s)
- Rob A. Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Melanie Müller
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Tom Berben
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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7
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Impey RE, Lee M, Hawkins DA, Sutton JM, Panjikar S, Perugini MA, Soares da Costa TP. Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens. FEBS Lett 2020; 594:1453-1463. [PMID: 31943170 DOI: 10.1002/1873-3468.13733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022]
Abstract
The rise of antibiotic resistance combined with the lack of new products entering the market has led to bacterial infections becoming one of the biggest threats to global health. Therefore, there is an urgent need to identify novel antibiotic targets, such as dihydrodipicolinate synthase (DHDPS), an enzyme involved in the production of essential metabolites in cell wall and protein synthesis. Here, we utilised a 7-residue sequence motif to identify mis-annotation of multiple DHDPS genes in the high-priority Gram-negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. We subsequently confirmed these mis-annotations using a combination of enzyme kinetics and X-ray crystallography. Thus, this study highlights the need to ensure genes encoding promising drug targets, like DHDPS, are annotated correctly, especially for clinically important pathogens. PDB ID: 6UE0.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Daniel A Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - J Mark Sutton
- National Infection Service, Research and Development Institute, Public Health England, Salisbury, UK
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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8
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Impey RE, Panjikar S, Hall CJ, Bock LJ, Sutton JM, Perugini MA, Soares da Costa TP. Identification of two dihydrodipicolinate synthase isoforms from Pseudomonas aeruginosa that differ in allosteric regulation. FEBS J 2019; 287:386-400. [PMID: 31330085 DOI: 10.1111/febs.15014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/12/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections, accounting for 10% of all hospital-acquired infections. Current antibiotics against P. aeruginosa are becoming increasingly ineffective due to the exponential rise in drug resistance. Thus, there is an urgent need to validate and characterize novel drug targets to guide the development of new classes of antibiotics against this pathogen. One such target is the diaminopimelate (DAP) pathway, which is responsible for the biosynthesis of bacterial cell wall and protein building blocks, namely meso-DAP and lysine. The rate-limiting step of this pathway is catalysed by the enzyme dihydrodipicolinate synthase (DHDPS), typically encoded for in bacteria by a single dapA gene. Here, we show that P. aeruginosa encodes two functional DHDPS enzymes, PaDHDPS1 and PaDHDPS2. Although these isoforms have similar catalytic activities (kcat = 29 s-1 and 44 s-1 for PaDHDPS1 and PaDHDPS2, respectively), they are differentially allosterically regulated by lysine, with only PaDHDPS2 showing inhibition by the end product of the DAP pathway (IC50 = 130 μm). The differences in allostery are attributed to a single amino acid difference in the allosteric binding pocket at position 56. This is the first example of a bacterium that contains multiple bona fide DHDPS enzymes, which differ in allosteric regulation. We speculate that the presence of the two isoforms allows an increase in the metabolic flux through the DAP pathway when required in this clinically important pathogen. DATABASES: PDB ID: 6P90.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lucy J Bock
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - J Mark Sutton
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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9
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Samainukul N, Linn AK, Javadi MB, Sakdee S, Angsuthanasombat C, Katzenmeier G. Importance of the Cys 124-Cys 128 intermolecular disulfide bonding for oligomeric assembly and hemolytic activity of the Helicobacter pylori TlyA hemolysin. Biochem Biophys Res Commun 2019; 514:365-371. [PMID: 31040022 DOI: 10.1016/j.bbrc.2019.04.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/13/2019] [Indexed: 01/16/2023]
Abstract
Although the TlyA hemolysin from Helicobacter pylori has been implicated as a potential virulence factor involved in mediating host cell colonization and hence disease progression, its structural determinants underlying the biological activity are still largely uncertain. In this study, an important role of the formation of a particular disulfide bond for functional oligomeric assembly of the H. pylori TlyA toxin was evidently elucidated. The 27-kDa TlyA recombinant protein was overexpressed in Escherichia coli, subsequently purified to near homogeneity by cation exchange chromatography, and proven to be hemolytically active against sheep erythrocytes. Additionally, TlyA-induced hemolytic activity was significantly diminished under conditions of disulfide bond reduction with a thiol-reducing agent, dithiothreitol. When the purified TlyA protein was subjected to modified SDS-PAGE under non-reducing conditions, the presence of an oligomeric state of this protein was clearly revealed by its apparent molecular mass of ∼48 kDa. Recombinant E. coli cells expressing TlyA also displayed contact-dependent hemolysis of erythrocytes, suggesting TlyA localization at the bacterial outer membrane and thus supporting the formation of disulfide-bonded TlyA. Homology-based modeling and in silico structural assembly analysis of TlyA signified potential intermolecular, rather than intramolecular, disulfide bonding through Cys124 and Cys128. Subsequently, single substitution of either of these Cys residues with Ser severely affected the oligomeric assembly of both TlyA mutants and hence abolished their hemolytic activity. Altogether, our present data provide pivotal evidence that the formation of intermolecular disulfide bonding between Cys124 and Cys128 plays a critical role in structural assembly of a biologically active-TlyA oligomer.
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Affiliation(s)
- Nitchakan Samainukul
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Aung Khine Linn
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Mohammad Bagher Javadi
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Somsri Sakdee
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Chanan Angsuthanasombat
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand; Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Gerd Katzenmeier
- Bacterial Toxin Reseach Innovation Cluster (BRIC), Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand.
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10
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Christoff RM, Gardhi CK, Soares da Costa TP, Perugini MA, Abbott BM. Pursuing DHDPS: an enzyme of unrealised potential as a novel antibacterial target. MEDCHEMCOMM 2019. [DOI: 10.1039/c9md00107g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DHDPS represents a novel enzyme target for the development of new antibiotics to combat multidrug resistance.
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Affiliation(s)
- Rebecca M. Christoff
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Chamodi K. Gardhi
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Belinda M. Abbott
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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11
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Ren W, Tao J, Shi D, Chen W, Chen C. Involvement of a dihydrodipicolinate synthase gene (FaDHDPS1) in fungal development, pathogenesis and stress responses in Fusarium asiaticum. BMC Microbiol 2018; 18:128. [PMID: 30290767 PMCID: PMC6173861 DOI: 10.1186/s12866-018-1268-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 09/27/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Dihydrodipicolinate synthase (DHDPS) is an allosteric enzyme, which catalyzes the first unique step of lysine biosynthesis in prokaryotes, higher plants and some fungi. To date, the biological roles of DHDPS in filamentous fungi are poorly understood. RESULTS In this study, on the basis of comparative genome resequencing, a DHDPS gene was found to be specific in Fusarium asiaticum, named FaDHDPS1, which showed high amino acid identity to that of entomopathogenic fungus. Subcellular localization of the FaDHDPS1-GFP fusion protein was mainly concentrated in the cytoplasm of conidia and dispersed in the cytoplasm during conidial germination. To reveal the biological functions, both deletion and complementation mutants of FaDHDPS1 were generated. The results showed that the FaDHDPS1 deletion mutant was defective in conidiation, virulence and DON biosynthesis. In addition, deletion of FaDHDPS1 resulted in tolerance to sodium pyruvate, lysine, low temperature and Congo red. CONCLUSION Results of this study indicate that FaDHDPS1 plays an important role in the regulation of vegetative differentiation, pathogenesis and adaption to multiple stresses in F. asiaticum.
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Affiliation(s)
- Weichao Ren
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Jiting Tao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Dongya Shi
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wenchan Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
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12
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Gupta R, Hogan CJ, Perugini MA, Soares da Costa TP. Characterization of recombinant dihydrodipicolinate synthase from the bread wheat Triticum aestivum. PLANTA 2018; 248:381-391. [PMID: 29744651 DOI: 10.1007/s00425-018-2894-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Recombinant wheat DHDPS was produced for the first time in milligram quantities and shown to be an enzymatically active tetramer in solution using analytical ultracentrifugation and small angle X-ray scattering. Wheat is an important cereal crop with an extensive role in global food supply. Given our rapidly growing population, strategies to increase the nutritional value and production of bread wheat are of major significance in agricultural science to satisfy our dietary requirements. Lysine is one of the most limiting essential amino acids in wheat, thus, a thorough understanding of lysine biosynthesis is of upmost importance to improve its nutritional value. Dihydrodipicolinate synthase (DHDPS; EC 4.3.3.7) catalyzes the first committed step in the lysine biosynthesis pathway of plants. Here, we report for the first time the expression and purification of recombinant DHDPS from the bread wheat Triticum aestivum (Ta-DHDPS). The optimized protocol yielded 36 mg of > 98% pure recombinant Ta-DHDPS per liter of culture. Enzyme kinetic studies demonstrate that the recombinant Ta-DHDPS has a KM (pyruvate) of 0.45 mM, KM (l-aspartate-4-semialdehyde) of 0.07 mM, kcat of 56 s-1, and is inhibited by lysine (IC 50 LYS of 0.033 mM), which agree well with previous studies using labor-intensive purification from wheat suspension cultures. We subsequently employed circular dichroism spectroscopy, analytical ultracentrifugation and small angle X-ray scattering to show that the recombinant enzyme is folded with 60% α/β structure and exists as a 7.5 S tetrameric species with a Rg of 33 Å and Dmax of 118 Å. This study is the first to report the biophysical properties of the recombinant Ta-DHDPS in aqueous solution and offers an excellent platform for future studies aimed at improving nutritional value and primary production of bread wheat.
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Affiliation(s)
- Ruchi Gupta
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Campbell J Hogan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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13
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Atkinson SC, Dogovski C, Wood K, Griffin MDW, Gorman MA, Hor L, Reboul CF, Buckle AM, Wuttke J, Parker MW, Dobson RCJ, Perugini MA. Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target. Structure 2018; 26:948-959.e5. [PMID: 29804823 DOI: 10.1016/j.str.2018.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/27/2018] [Accepted: 04/19/2018] [Indexed: 11/19/2022]
Abstract
Protein dynamics manifested through structural flexibility play a central role in the function of biological molecules. Here we explore the substrate-mediated change in protein flexibility of an antibiotic target enzyme, Clostridium botulinum dihydrodipicolinate synthase. We demonstrate that the substrate, pyruvate, stabilizes the more active dimer-of-dimers or tetrameric form. Surprisingly, there is little difference between the crystal structures of apo and substrate-bound enzyme, suggesting protein dynamics may be important. Neutron and small-angle X-ray scattering experiments were used to probe substrate-induced dynamics on the sub-second timescale, but no significant changes were observed. We therefore developed a simple technique, coined protein dynamics-mass spectrometry (ProD-MS), which enables measurement of time-dependent alkylation of cysteine residues. ProD-MS together with X-ray crystallography and analytical ultracentrifugation analyses indicates that pyruvate locks the conformation of the dimer that promotes docking to the more active tetrameric form, offering insight into ligand-mediated stabilization of multimeric enzymes.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lilian Hor
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Melbourne, VIC 3086, Australia
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joachim Wuttke
- Juelich Centre for Neutron Science (JCNS), at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenstrasse 1, Garching 85 747, Germany
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag, Christchurch 4800, New Zealand
| | - Matthew A Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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14
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Desbois S, John UP, Perugini MA. Dihydrodipicolinate synthase is absent in fungi. Biochimie 2018; 152:73-84. [PMID: 29959064 DOI: 10.1016/j.biochi.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
The class I aldolase dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step of the diaminopimelate (DAP) lysine biosynthesis pathway in bacteria, archaea and plants. Despite the existence, in databases, of numerous fungal sequences annotated as DHDPS, its presence in fungi has been the subject of contradictory claims. We report the characterization of DHDPS candidates from fungi. Firstly, the putative DHDPS from Coccidioides immitis (PDB ID: 3QFE) was shown to have negligible enzyme activity. Sequence analysis of 3QFE showed that three out of the seven amino acid residues critical for DHDPS activity are absent; however, exact matches to catalytic residues from two other class I aldolases, 2-keto-3-deoxygluconate aldolase (KDGA), and 4-hydroxy-2-oxoglutarate aldolase (HOGA), were identified. The presence of both KDGA and HOGA activity in 3QFE was confirmed in vitro using enzyme assays, the first report of such dual activity. Subsequent analyses of all publically available fungal sequences revealed that no entry contains all seven residues important for DHDPS function. The candidate with the highest number of identities (6 of 7), KIW77228 from Fonsecaea pedrosoi, was shown to have trace DHDPS activity in vitro, partially restored by substitution of the seventh critical residue, and to be incapable of complementing DHDPS-deficient E. coli cells. Combined with the presence of all seven sequences for the alternative α-aminoadipate (AAA) lysine biosynthesis pathway in C. immitis and F. pedrosoi, we believe that DHDPS and the DAP pathway are absent in fungi, and further, that robust informed methods for annotating genes need to be implemented.
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Affiliation(s)
- Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia
| | - Ulrik P John
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia; Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe University, VIC, 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia.
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15
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Soares da Costa TP, Abbott BM, Gendall AR, Panjikar S, Perugini MA. Molecular evolution of an oligomeric biocatalyst functioning in lysine biosynthesis. Biophys Rev 2018; 10:153-162. [PMID: 29204887 PMCID: PMC5899710 DOI: 10.1007/s12551-017-0350-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 12/28/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) is critical to the production of lysine through the diaminopimelate (DAP) pathway. Elucidation of the function, regulation and structure of this key class I aldolase has been the focus of considerable study in recent years, given that the dapA gene encoding DHDPS has been found to be essential to bacteria and plants. Allosteric inhibition by lysine is observed for DHDPS from plants and some bacterial species, the latter requiring a histidine or glutamate at position 56 (Escherichia coli numbering) over a basic amino acid. Structurally, two DHDPS monomers form the active site, which binds pyruvate and (S)-aspartate β-semialdehyde, with most dimers further dimerising to form a tetrameric arrangement around a solvent-filled centre cavity. The architecture and behaviour of these dimer-of-dimers is explored in detail, including biophysical studies utilising analytical ultracentrifugation, small-angle X-ray scattering and macromolecular crystallography that show bacterial DHDPS tetramers adopt a head-to-head quaternary structure, compared to the back-to-back arrangement observed for plant DHDPS enzymes. Finally, the potential role of pyruvate in providing substrate-mediated stabilisation of DHDPS is considered.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Melbourne, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC, 3800, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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16
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Gupta R, Soares da Costa TP, Faou P, Dogovski C, Perugini MA. Comparison of untagged and his-tagged dihydrodipicolinate synthase from the enteric pathogen Vibrio cholerae. Protein Expr Purif 2018; 145:85-93. [PMID: 29337198 DOI: 10.1016/j.pep.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/02/2018] [Accepted: 01/10/2018] [Indexed: 02/03/2023]
Abstract
Given the emergence of multi drug resistant Vibrio cholerae strains, there is an urgent need to characterize new anti-cholera targets. One such target is the enzyme dihydrodipicolinate synthase (DHDPS; EC 4.3.3.7), which catalyzes the first committed step in the diaminopimelate pathway. This pathway is responsible for the production of two key metabolites in bacteria and plants, namely meso-2,6-diaminopimelate and L-lysine. Here, we report the cloning, expression and purification of untagged and His-tagged recombinant DHDPS from V. cholerae (Vc-DHDPS) and provide comparative structural and kinetic analyses. Structural studies employing circular dichroism spectroscopy and analytical ultracentrifugation demonstrate that the recombinant enzymes are folded and exist as dimers in solution. Kinetic analyses of untagged and His-tagged Vc-DHDPS show that the enzymes are functional with specific activities of 75.6 U/mg and 112 U/mg, KM (pyruvate) of 0.14 mM and 0.15 mM, KM (L-aspartate-4-semialdehyde) of 0.08 mM and 0.09 mM, and kcat of 34 and 46 s-1, respectively. These results demonstrate there are no significant changes in the structure and function of Vc-DHDPS upon the addition of an N-terminal His tag and, hence, the tagged recombinant product is suitable for future studies, including screening for new inhibitors as potential anti-cholera agents. Additionally, a polyclonal antibody raised against untagged Vc-DHDPS is validated for specifically detecting recombinant and native forms of the enzyme.
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Affiliation(s)
- Ruchi Gupta
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Con Dogovski
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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17
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Chaturvedi SK, Ma J, Zhao H, Schuck P. Use of fluorescence-detected sedimentation velocity to study high-affinity protein interactions. Nat Protoc 2017; 12:1777-1791. [PMID: 28771239 PMCID: PMC7466938 DOI: 10.1038/nprot.2017.064] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sedimentation velocity (SV) analytical ultracentrifugation (AUC) is a classic technique for the real-time observation of free macromolecular migration in solution driven by centrifugal force. This enables the analysis of macromolecular mass, shape, size distribution, and interactions. Although traditionally limited to determination of the sedimentation coefficient and binding affinity of proteins in the micromolar range, the implementation of modern detection and data analysis techniques has resulted in marked improvements in detection sensitivity and size resolution during the past decades. Fluorescence optical detection now permits the detection of recombinant proteins with fluorescence excitation at 488 or 561 nm at low picomolar concentrations, allowing for the study of high-affinity protein self-association and hetero-association. Compared with other popular techniques for measuring high-affinity protein-protein interactions, such as biosensing or calorimetry, the high size resolution of complexes at picomolar concentrations obtained with SV offers a distinct advantage in sensitivity and flexibility of the application. Here, we present a basic protocol for carrying out fluorescence-detected SV experiments and the determination of the size distribution and affinity of protein-antibody complexes with picomolar KD values. Using an EGFP-nanobody interaction as a model, this protocol describes sample preparation, ultracentrifugation, data acquisition, and data analysis. A variation of the protocol applying traditional absorbance or an interference optical system can be used for protein-protein interactions in the micromolar KD value range. Sedimentation experiments typically take ∼3 h of preparation and 6-12 h of run time, followed by data analysis (typically taking 1-3 h).
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Affiliation(s)
- Sumit K. Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
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18
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Soares da Costa TP, Patel M, Desbois S, Gupta R, Faou P, Perugini MA. Identification of a dimeric KDG aldolase from
Agrobacterium tumefaciens. Proteins 2017; 85:2058-2065. [DOI: 10.1002/prot.25359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Tatiana P. Soares da Costa
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Madhvi Patel
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Sebastien Desbois
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Ruchi Gupta
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Pierre Faou
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Matthew A. Perugini
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
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19
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Guérin J, Bigot S, Schneider R, Buchanan SK, Jacob-Dubuisson F. Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions. Front Cell Infect Microbiol 2017; 7:148. [PMID: 28536673 PMCID: PMC5422565 DOI: 10.3389/fcimb.2017.00148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022] Open
Abstract
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
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Affiliation(s)
- Jeremy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, Centre National de La Recherche Scientifique UMR 5086-Université Lyon 1, Institute of Biology and Chemistry of ProteinsLyon, France
| | - Robert Schneider
- NMR and Molecular Interactions, Université de Lille, Centre National de La Recherche Scientifique, UMR 8576-Unité de Glycobiologie Structurale et FonctionnelleLille, France
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Françoise Jacob-Dubuisson
- Université de Lille, Centre National de La Recherche Scientifique, Institut National de La Santé et de La Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-Centre d'Infection et d'Immunité de LilleLille, France
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20
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Grant Pearce F, Hudson AO, Loomes K, Dobson RCJ. Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution. Subcell Biochem 2017; 83:271-289. [PMID: 28271480 DOI: 10.1007/978-3-319-46503-6_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Enzymes are usually comprised of multiple subunits and more often than not they are made up of identical subunits. In this review we examine lysine biosynthesis and focus on the enzyme dihydrodipicolinate synthase in terms of its structure, function and the evolution of its varied number of subunits (quaternary structure). Dihydrodipicolinate synthase is the first committed step in the biosynthesis of lysine, which occurs naturally in plants, bacteria, archaea and fungi, but is not synthesized in mammals. In bacteria, there have been four separate pathways identified from tetrahydrodipicolinate to meso-diaminopimelate, which is the immediate precursor to lysine. Dihydrodipicolinate synthases from many bacterial and plant species have been structurally characterised and the results show considerable variability with respect to their quaternary structure, hinting at their evolution. The oligomeric state of the enzyme plays a key role, both in catalysis and in the allosteric regulation of the enzyme by lysine. While most bacteria and plants have tetrameric enzymes, where the structure of the dimeric building blocks is conserved, the arrangement of the dimers differs. We also review a key development in the field, namely the discovery of a human dihydrodipicolinate synthase-like enzyme, now known as 4-hydroxy-2-oxoglutarate aldolase . This discovery complicates the rationale underpinning drug development against bacterial dihydrodipicolinate synthases, since genetic errors in 4-hydroxy-2-oxoglutarate aldolase cause the disease Primary Hyperoxaluria Type 3 and therefore compounds that are geared towards the inhibition of bacterial dihydrodipicolinate synthase may be toxic to mammalian cells.
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Affiliation(s)
- F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Kerry Loomes
- School of Biological Sciences & Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8041, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia.
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21
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Christensen JB, Soares da Costa TP, Faou P, Pearce FG, Panjikar S, Perugini MA. Structure and Function of Cyanobacterial DHDPS and DHDPR. Sci Rep 2016; 6:37111. [PMID: 27845445 PMCID: PMC5109050 DOI: 10.1038/srep37111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 11/21/2022] Open
Abstract
Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.
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Affiliation(s)
- Janni B. Christensen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - T. P. Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - F. Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Victoria 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
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22
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North RA, Watson AJA, Pearce FG, Muscroft-Taylor AC, Friemann R, Fairbanks AJ, Dobson RCJ. Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. FEBS Lett 2016; 590:4414-4428. [PMID: 27943302 DOI: 10.1002/1873-3468.12462] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/09/2016] [Indexed: 01/07/2023]
Abstract
N-Acetylneuraminate lyase is the first committed enzyme in the degradation of sialic acid by bacterial pathogens. In this study, we analyzed the kinetic parameters of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus (MRSA). We determined that the enzyme has a relatively high KM of 3.2 mm, suggesting that flux through the catabolic pathway is likely to be controlled by this enzyme. Our data indicate that sialic acid alditol, a known inhibitor of N-acetylneuraminate lyase enzymes, is a stronger inhibitor of MRSA N-acetylneuraminate lyase than of Clostridium perfringens N-acetylneuraminate lyase. Our analysis of the crystal structure of ligand-free and 2R-sialic acid alditol-bound MRSA N-acetylneuraminate lyase suggests that subtle dynamic differences in solution and/or altered binding interactions within the active site may account for species-specific inhibition.
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Affiliation(s)
- Rachel A North
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew J A Watson
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew C Muscroft-Taylor
- Protein Science and Engineering, Callaghan Innovation, University of Canterbury, Christchurch, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Sweden.,Department of Structural Biology, School of Medicine, Stanford University, CA, USA
| | - Antony J Fairbanks
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
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23
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Soares da Costa TP, Desbois S, Dogovski C, Gorman MA, Ketaren NE, Paxman JJ, Siddiqui T, Zammit LM, Abbott BM, Robins-Browne RM, Parker MW, Jameson GB, Hall NE, Panjikar S, Perugini MA. Structural Determinants Defining the Allosteric Inhibition of an Essential Antibiotic Target. Structure 2016; 24:1282-1291. [PMID: 27427481 DOI: 10.1016/j.str.2016.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/22/2016] [Accepted: 05/06/2016] [Indexed: 11/29/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine biosynthesis pathway of bacteria. The pathway can be regulated by feedback inhibition of DHDPS through the allosteric binding of the end product, lysine. The current dogma states that DHDPS from Gram-negative bacteria are inhibited by lysine but orthologs from Gram-positive species are not. The 1.65-Å resolution structure of the Gram-negative Legionella pneumophila DHDPS and the 1.88-Å resolution structure of the Gram-positive Streptococcus pneumoniae DHDPS bound to lysine, together with comprehensive functional analyses, show that this dogma is incorrect. We subsequently employed our crystallographic data with bioinformatics, mutagenesis, enzyme kinetics, and microscale thermophoresis to reveal that lysine-mediated inhibition is not defined by Gram staining, but by the presence of a His or Glu at position 56 (Escherichia coli numbering). This study has unveiled the molecular determinants defining lysine-mediated allosteric inhibition of bacterial DHDPS.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Con Dogovski
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Natalia E Ketaren
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Tanzeela Siddiqui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Leanne M Zammit
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia; Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Geoffrey B Jameson
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Nathan E Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, VIC 3168, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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24
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Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein. mBio 2016; 7:e02046. [PMID: 26980835 PMCID: PMC4807369 DOI: 10.1128/mbio.02046-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Urinary tract infection (UTI) is a disease of extremely high incidence in both community and nosocomial settings. UTIs cause significant morbidity and mortality, with approximately 150 million cases globally per year. Uropathogenic Escherichia coli (UPEC) is the primary cause of UTI and is generally treated empirically. However, the rapidly increasing incidence of UTIs caused by multidrug-resistant UPEC strains has led to limited available treatment options and highlights the urgent need to develop alternative treatment and prevention strategies. In this study, we performed a comprehensive analysis to define the regulation, structure, function, and immunogenicity of recently identified UPEC vaccine candidate C1275 (here referred to as IrmA). We showed that the irmA gene is highly prevalent in UPEC, is cotranscribed with the biofilm-associated antigen 43 gene, and is regulated by the global oxidative stress response OxyR protein. Localization studies identified IrmA in the UPEC culture supernatant. We determined the structure of IrmA and showed that it adopts a unique domain-swapped dimer architecture. The dimeric structure of IrmA displays similarity to those of human cytokine receptors, including the interleukin-2 receptor (IL-2R), interleukin-4 receptor (IL-4R), and interleukin-10 receptor (IL-10R) binding domains, and we showed that purified IrmA can bind to their cognate cytokines. Finally, we showed that plasma from convalescent urosepsis patients contains high IrmA antibody titers, demonstrating the strong immunogenicity of IrmA. Taken together, our results indicate that IrmA may play an important role during UPEC infection. Uropathogenic E. coli (UPEC) is the primary cause of urinary tract infection (UTI), a disease of major significance to human health. Globally, the incidence of UPEC-mediated UTI is strongly associated with increasing antibiotic resistance, making this extremely common infection a major public health concern. In this report, we describe the regulatory, structural, functional, and immunogenic properties of a candidate UPEC vaccine antigen, IrmA. We demonstrate that IrmA is a small UPEC protein that forms a unique domain-swapped dimer with structural mimicry to several human cytokine receptors. We also show that IrmA binds to IL-2, IL-4, and IL-10, is strongly immunogenic in urosepsis patients, and is coexpressed with factors associated with biofilm formation. Overall, this work suggests a potential novel contribution for IrmA in UPEC infection.
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25
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Gordon SE, Weber DK, Downton MT, Wagner J, Perugini MA. Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation. PLoS Comput Biol 2016; 12:e1004811. [PMID: 26967332 PMCID: PMC4788353 DOI: 10.1371/journal.pcbi.1004811] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/12/2016] [Indexed: 11/29/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions. Interactions between proteins and ligands underpin many important biological processes, such as binding of substrates to their cognate enzymes in the process of catalysis. These interactions are complex, often requiring several intermediate steps to fully transition into the bound state. Here, we have used computational simulation to study binding of pyruvate to Dihydrodipicolinate synthase (DHDPS), an enzyme in the bacterial diaminopimelate pathway. In bacteria, such as the human pathogen S. aureus, DHDPS functions to make building blocks necessary for protein and bacterial cell wall biosyntheses. As the enzyme is absent in humans, yet essential for bacterial growth, DHDPS is a valid target for broad-range antibiotics. However, known DHDPS inhibitors show poor potency. One avenue that has not yet been taken into consideration for inhibitor design is the dynamics of DHDPS’s interaction with its reaction substrates (e.g. pyruvate). Using molecular dynamics simulation, we find that pyruvate binding to DHDPS must pass through a transition intermediate ‘hotspot’ in which the substrate is held in place by a dense network of noncovalent bonds. Given that many of the protein residues involved in this interaction are also shared by DHDPS from many pathogenic bacteria, this binding intermediate ‘hotspot’ may help in development of better broad-range DHDPS inhibitors.
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Affiliation(s)
- Shane E. Gordon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Computational Biophysics, IBM Research - Australia, Carlton, Victoria, Australia
| | - Daniel K. Weber
- Computational Biophysics, IBM Research - Australia, Carlton, Victoria, Australia
| | - Matthew T. Downton
- Computational Biophysics, IBM Research - Australia, Carlton, Victoria, Australia
| | - John Wagner
- Computational Biophysics, IBM Research - Australia, Carlton, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- * E-mail:
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26
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Peverelli MG, Soares da Costa TP, Kirby N, Perugini MA. Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis. J Biol Chem 2016; 291:9785-95. [PMID: 26921318 DOI: 10.1074/jbc.m115.696591] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/06/2022] Open
Abstract
Diaminopimelate decarboxylase (DAPDC) catalyzes the final step in the diaminopimelate biosynthesis pathway of bacteria. The product of the reaction is the essential amino acid l-lysine, which is an important precursor for the synthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Accordingly, the enzyme is a promising antibacterial target. Previous structural studies demonstrate that DAPDC exists as monomers, dimers, and tetramers in the crystal state. However, the active oligomeric form has not yet been determined. We show using analytical ultracentrifugation, small angle x-ray scattering, and enzyme kinetic analyses in solution that the active form of DAPDC from Bacillus anthracis, Escherichia coli, Mycobacterium tuberculosis, and Vibrio cholerae is a dimer. The importance of dimerization was probed further by generating dimerization interface mutants (N381A and R385A) of V. cholerae DAPDC. Our studies indicate that N381A and R385A are significantly attenuated in catalytic activity, thus confirming that dimerization of DAPDC is essential for function. These findings provide scope for the development of new antibacterial agents that prevent DAPDC dimerization.
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Affiliation(s)
- Martin G Peverelli
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria 3010, and
| | - Tatiana P Soares da Costa
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Nigel Kirby
- the The Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Matthew A Perugini
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria 3010, and
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27
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Naqvi KF, Staker BL, Dobson RCJ, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO. Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:2-9. [PMID: 26750477 PMCID: PMC4708043 DOI: 10.1107/s2053230x15023213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were Rr.i.m. = 0.098, Rwork = 0.183, Rfree = 0.233.
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Affiliation(s)
- Kubra F. Naqvi
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Dmitry Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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28
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Abstract
Here, we review recent studies aimed at defining the importance of quaternary structure to a model oligomeric enzyme, dihydrodipicolinate synthase. This will illustrate the complementary and synergistic outcomes of coupling the techniques of analytical ultracentrifugation with enzyme kinetics, in vitro mutagenesis, macromolecular crystallography, small angle X-ray scattering, and molecular dynamics simulations, to demonstrate the role of subunit self-association in facilitating protein dynamics and enzyme function. This multitechnique approach has yielded new insights into the molecular evolution of protein quaternary structure.
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29
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Peverelli MG, Perugini MA. An optimized coupled assay for quantifying diaminopimelate decarboxylase activity. Biochimie 2015; 115:78-85. [PMID: 25986217 DOI: 10.1016/j.biochi.2015.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-DAP to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway in plants and bacteria. Given its absence in humans, DAPDC is a promising antibacterial target, particularly considering the rise in drug-resistant strains from pathogens such as Escherichia coli and Mycobacterium tuberculosis. Here, we report the optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) as the coupling enzyme. Our results show that SDH has optimal activity at 37 °C, pH 8.0, and in Tris buffer. These conditions were subsequently employed to quantitate the enzyme kinetic properties of DAPDC from three bacterial species. We show that DAPDC from E. coli and M. tuberculosis have [Formula: see text] of 0.97 mM and 1.62 mM and a kcat of 55 s(-1) and 28 s(-1), respectively, which agree well with previous studies using more labor-intensive assays. We subsequently employed the optimized coupled assay to show for the first time that DAPDC from Bacillus anthracis possesses a [Formula: see text] of 0.68 mM and a kcat of 58 s(-1). This optimized coupled assay offers excellent scope to be employed in high throughput drug discovery screens targeting DAPDC from bacterial pathogens.
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Affiliation(s)
- Martin G Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew A Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
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30
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Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus. Extremophiles 2014; 18:973-85. [PMID: 24996798 DOI: 10.1007/s00792-014-0667-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS, E.C.4.2.1.52) catalyzes the first committed step in the lysine biosynthetic pathway: the condensation of (S)-aspartate semialdehyde and pyruvate to form (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. Since (S)-lysine biosynthesis does not occur in animals, DHDPS is an attractive target for rational antibiotic and herbicide design. Here, we report the crystal structure of DHDPS from a hyperthermophilic bacterium Aquifex aeolicus (AqDHDPS). L-Lysine is used as an important animal feed additive where the production is at the level of 1.5 million tons per year. The biotechnological manufacture of lysine has been going for more than 50 years which includes over synthesis and reverse engineering of DHDPS. AqDHDPS revealed a unique disulfide linkage which is not conserved in the homologues of AqDHDPS. In silico mutation of C139A and intermolecular ion-pair residues and the subsequent molecular dynamics simulation of the mutants showed that these residues are critical for the stability of AqDHDPS tetramer. MD simulations of AqDHDPS at three different temperatures (303, 363 and 393 K) revealed that the molecule is stable at 363 K. Thus, this structural and in silico study of AqDHDPS likely provides additional details towards the rational and structure-based design of hyper-L-lysine producing bacterial strains.
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31
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Atkinson SC, Hor L, Dogovski C, Dobson RCJ, Perugini MA. Identification of the bona fide DHDPS from a common plant pathogen. Proteins 2014; 82:1869-83. [PMID: 24677246 DOI: 10.1002/prot.24539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 01/06/2014] [Accepted: 02/13/2014] [Indexed: 11/10/2022]
Abstract
Agrobacterium tumefaciens is a Gram-negative soil-borne bacterium that causes Crown Gall disease in many economically important crops. The absence of a suitable chemical treatment means there is a need to discover new anti-Crown Gall agents and also characterize bona fide drug targets. One such target is dihydrodipicolinate synthase (DHDPS), a homo-tetrameric enzyme that catalyzes the committed step in the metabolic pathway yielding meso-diaminopimelate and lysine. Interestingly, there are 10 putative DHDPS genes annotated in the A. tumefaciens genome, including three whose structures have recently been determined (PDB IDs: 3B4U, 2HMC, and 2R8W). However, we show using quantitative enzyme kinetic assays that nine of the 10 dapA gene products, including 3B4U, 2HMC, and 2R8W, lack DHDPS function in vitro. A sequence alignment showed that the product of the dapA7 gene contains all of the conserved residues known to be important for DHDPS catalysis and allostery. This gene was cloned and the recombinant product expressed and purified. Our studies show that the purified enzyme (i) possesses DHDPS enzyme activity, (ii) is allosterically inhibited by lysine, and (iii) adopts the canonical homo-tetrameric structure in both solution and the crystal state. This study describes for the first time the structure, function and allostery of the bona fide DHDPS from A. tumefaciens, which offers insight into the rational design of pesticide agents for combating Crown Gall disease.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
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32
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Dogovski C, Gorman MA, Ketaren NE, Praszkier J, Zammit LM, Mertens HD, Bryant G, Yang J, Griffin MDW, Pearce FG, Gerrard JA, Jameson GB, Parker MW, Robins-Browne RM, Perugini MA. From knock-out phenotype to three-dimensional structure of a promising antibiotic target from Streptococcus pneumoniae. PLoS One 2013; 8:e83419. [PMID: 24349508 PMCID: PMC3862839 DOI: 10.1371/journal.pone.0083419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/13/2013] [Indexed: 11/18/2022] Open
Abstract
Given the rise in drug-resistant Streptococcus pneumoniae, there is an urgent need to discover new antimicrobials targeting this pathogen and an equally urgent need to characterize new drug targets. A promising antibiotic target is dihydrodipicolinate synthase (DHDPS), which catalyzes the rate-limiting step in lysine biosynthesis. In this study, we firstly show by gene knock out studies that S. pneumoniae (sp) lacking the DHDPS gene is unable to grow unless supplemented with lysine-rich media. We subsequently set out to characterize the structure, function and stability of the enzyme drug target. Our studies show that sp-DHDPS is folded and active with a k(cat) = 22 s(-1), K(M)(PYR) = 2.55 ± 0.05 mM and K(M)(ASA) = 0.044 ± 0.003 mM. Thermal denaturation experiments demonstrate sp-DHDPS exhibits an apparent melting temperature (T(M)(app)) of 72 °C, which is significantly greater than Escherichia coli DHDPS (Ec-DHDPS) (T(M)(app) = 59 °C). Sedimentation studies show that sp-DHDPS exists in a dimer-tetramer equilibrium with a K(D)(4→2) = 1.7 nM, which is considerably tighter than its E. coli ortholog (K(D)(4→2) = 76 nM). To further characterize the structure of the enzyme and probe its enhanced stability, we solved the high resolution (1.9 Å) crystal structure of sp-DHDPS (PDB ID 3VFL). The enzyme is tetrameric in the crystal state, consistent with biophysical measurements in solution. Although the sp-DHDPS and Ec-DHDPS active sites are almost identical, the tetramerization interface of the s. pneumoniae enzyme is significantly different in composition and has greater buried surface area (800 Å(2)) compared to its E. coli counterpart (500 Å(2)). This larger interface area is consistent with our solution studies demonstrating that sp-DHDPS is considerably more thermally and thermodynamically stable than Ec-DHDPS. Our study describe for the first time the knock-out phenotype, solution properties, stability and crystal structure of DHDPS from S. pneumoniae, a promising antimicrobial target.
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Affiliation(s)
- Con Dogovski
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Michael A. Gorman
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Natalia E. Ketaren
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Judy Praszkier
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Leanne M. Zammit
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Gary Bryant
- School of Applied Sciences, RMIT University, Melbourne, Victoria, Australia
| | - Ji Yang
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - F. Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Callaghan Innovation, Lower Hutt, New Zealand
| | - Geoffrey B. Jameson
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Roy M. Robins-Browne
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
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33
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Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW. Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase fromStaphylococcus aureus. Mol Microbiol 2013; 91:110-20. [DOI: 10.1111/mmi.12446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Min Y. Yap
- School of Biomedical Science; Monash University; Victoria 3800 Australia
| | - Matthew A. Perugini
- Department of Biochemistry; La Trobe Institute for Molecular Science; La Trobe University; Victoria 3086 Australia
| | - John C. Wallace
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- School of Chemistry and Physics; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | | | - Steven W. Polyak
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
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34
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Siddiqui T, Paxman JJ, Dogovski C, Panjikar S, Perugini MA. Cloning to crystallization of dihydrodipicolinate synthase from the intracellular pathogen Legionella pneumophila. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1177-81. [PMID: 24100576 PMCID: PMC3792684 DOI: 10.1107/s1744309113024639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 09/03/2013] [Indexed: 11/11/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyses the rate-limiting step in the biosynthesis of meso-diaminopimelate and lysine. Here, the cloning, expression, purification and crystallization of DHDPS from the intracellular pathogen Legionella pneumophila are described. Crystals grown in the presence of high-molecular-weight PEG precipitant and magnesium chloride were found to diffract beyond 1.65 Å resolution. The crystal lattice belonged to the hexagonal space group P6₁22, with unit-cell parameters a=b=89.31, c=290.18 Å, and contained two molecules in the asymmetric unit. The crystal structure was determined by molecular replacement using a single chain of Pseudomonas aeruginosa DHDPS as the search model.
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Affiliation(s)
- Tanzeela Siddiqui
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, VIC 3010, Australia
| | | | - Con Dogovski
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, VIC 3010, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, VIC 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC 3800, Australia
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, VIC 3010, Australia
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Atkinson SC, Dogovski C, Downton MT, Czabotar PE, Dobson RCJ, Gerrard JA, Wagner J, Perugini MA. Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition. PLANT MOLECULAR BIOLOGY 2013; 81:431-446. [PMID: 23354837 DOI: 10.1007/s11103-013-0014-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/15/2013] [Indexed: 06/01/2023]
Abstract
Lysine is one of the most limiting amino acids in plants and its biosynthesis is carefully regulated through inhibition of the first committed step in the pathway catalyzed by dihydrodipicolinate synthase (DHDPS). This is mediated via a feedback mechanism involving the binding of lysine to the allosteric cleft of DHDPS. However, the precise allosteric mechanism is yet to be defined. We present a thorough enzyme kinetic and thermodynamic analysis of lysine inhibition of DHDPS from the common grapevine, Vitis vinifera (Vv). Our studies demonstrate that lysine binding is both tight (relative to bacterial DHDPS orthologs) and cooperative. The crystal structure of the enzyme bound to lysine (2.4 Å) identifies the allosteric binding site and clearly shows a conformational change of several residues within the allosteric and active sites. Molecular dynamics simulations comparing the lysine-bound (PDB ID 4HNN) and lysine free (PDB ID 3TUU) structures show that Tyr132, a key catalytic site residue, undergoes significant rotational motion upon lysine binding. This suggests proton relay through the catalytic triad is attenuated in the presence of lysine. Our study reveals for the first time the structural mechanism for allosteric inhibition of DHDPS from the common grapevine.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
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Erzeel E, Van Bochaute P, Thu TT, Angenon G. Medicago truncatula dihydrodipicolinate synthase (DHDPS) enzymes display novel regulatory properties. PLANT MOLECULAR BIOLOGY 2013; 81:401-415. [PMID: 23329373 DOI: 10.1007/s11103-013-0008-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 01/04/2013] [Indexed: 06/01/2023]
Abstract
Lysine biosynthesis in plants is tightly regulated by feedback inhibition of the end product on the first enzyme of the lysine-specific branch, dihydrodipicolinate synthase (DHDPS). Three complete DHDPS coding sequences and one partial sequence were obtained in Medicago truncatula via inverse PCR. Analysis of the MtDHDPS sequences indicated the presence of isozymes (MtDHDPS2 and MtDHDPS3) with multiple amino acid substitutions on positions previously shown to be involved in feedback inhibition and of residues important for catalytic activity, possibly affecting the enzymatic properties of these isoforms. Sequences similar to MtDHDPS2 and 3 are present in Lotus japonicus and Glycine max, suggesting the existence of a specific conserved class of DHDPS genes within the Fabaceae family. The MtDHDPS genes were found by quantitative RT-PCR analysis to be expressed in an organ-specific manner in M. truncatula. All four MtDHDPS enzymes were expressed separately in Escherichia coli, revealing a strongly reduced sensitivity of the MtDHDPS2 protein to lysine feedback inhibition and a severely reduced activity of the MtDHDPS3 protein. Remarkably, MtDHDPS3 expression in Arabidopsis thaliana produced transgenic plants with a significantly increased threonine level, suggesting a dominant DHDPS inhibiting role of this isoform. This is supported by co-expression experiments in E. coli which indicate that AtDHDPS and MtDHDPS3 interact and may form hetero-oligomers with strongly reduced enzymatic activity. In conclusion, analysis of DHDPS in M. truncatula revealed the presence of unique isozymes displaying novel regulatory properties.
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Affiliation(s)
- Ellen Erzeel
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium
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37
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North RA, Kessans SA, Atkinson SC, Suzuki H, Watson AJA, Burgess BR, Angley LM, Hudson AO, Varsani A, Griffin MDW, Fairbanks AJ, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:306-12. [PMID: 23519810 PMCID: PMC3606580 DOI: 10.1107/s1744309113003060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/30/2013] [Indexed: 01/13/2023]
Abstract
The enzyme N-acetylneuraminate lyase (EC 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-D-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic DNA, and recombinant protein was expressed and purified from Escherichia coli BL21 (DE3). The enzyme crystallized in a number of crystal forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.70 Å resolution in space group P2₁. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights for the development of future antimicrobials.
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Affiliation(s)
- Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Andrew J. A. Watson
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Benjamin R. Burgess
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Lauren M. Angley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Arvind Varsani
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Antony J. Fairbanks
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
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Hor L, Dobson RCJ, Downton MT, Wagner J, Hutton CA, Perugini MA. Dimerization of bacterial diaminopimelate epimerase is essential for catalysis. J Biol Chem 2013; 288:9238-48. [PMID: 23426375 DOI: 10.1074/jbc.m113.450148] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Diaminopimelate (DAP) epimerase is involved in the biosynthesis of meso-DAP and lysine, which are important precursors for the synthesis of peptidoglycan, housekeeping proteins, and virulence factors in bacteria. Accordingly, DAP epimerase is a promising antimicrobial target. Previous studies report that DAP epimerase exists as a monomeric enzyme. However, we show using analytical ultracentrifugation, X-ray crystallography, and enzyme kinetic analyses that DAP epimerase from Escherichia coli exists as a functional dimer in solution and the crystal state. Furthermore, the 2.0-Å X-ray crystal structure of the E. coli DAP epimerase dimer shows for the first time that the enzyme exists in an open, active conformation. The importance of dimerization was subsequently probed by using site-directed mutagenesis to generate a monomeric mutant (Y268A). Our studies show that Y268A is catalytically inactive, thus demonstrating that dimerization of DAP epimerase is essential for catalysis. Molecular dynamics simulations indicate that the DAP epimerase monomer is inherently more flexible than the dimer, suggesting that dimerization optimizes protein dynamics to support function. Our findings offer insight into the development of novel antimicrobial agents targeting the dimeric antibiotic target DAP epimerase.
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Affiliation(s)
- Lilian Hor
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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39
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Comparative structure and function analyses of native and his-tagged forms of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus. Protein Expr Purif 2012; 85:66-76. [DOI: 10.1016/j.pep.2012.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/25/2012] [Accepted: 06/27/2012] [Indexed: 11/22/2022]
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40
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Atkinson SC, Dogovski C, Dobson RCJ, Perugini MA. Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from Agrobacterium tumefaciens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1040-7. [PMID: 22949190 PMCID: PMC3433193 DOI: 10.1107/s1744309112033052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/20/2012] [Indexed: 11/10/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of DHDPS (NP_354047.1) from the plant pathogen Agrobacterium tumefaciens (AgT-DHDPS). Enzyme-kinetics studies demonstrate that AgT-DHDPS possesses DHDPS activity in vitro. Crystals of AgT-DHDPS were grown in the unliganded form and in forms with substrate bound and with substrate plus allosteric inhibitor (lysine) bound. X-ray diffraction data sets were subsequently collected to a maximum resolution of 1.40 Å. Determination of the structure with and without substrate and inhibitor will offer insight into the design of novel pesticide agents.
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Affiliation(s)
- Sarah C. Atkinson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia
| | - Con Dogovski
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria 3010, Australia
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41
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Griffin MDW, Billakanti JM, Wason A, Keller S, Mertens HDT, Atkinson SC, Dobson RCJ, Perugini MA, Gerrard JA, Pearce FG. Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana. PLoS One 2012; 7:e40318. [PMID: 22792278 PMCID: PMC3390394 DOI: 10.1371/journal.pone.0040318] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/04/2012] [Indexed: 11/19/2022] Open
Abstract
In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS) and dihydrodipicolinate reductase (DHDPR) catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2) has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S)-lysine. Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2) has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.
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Affiliation(s)
- Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jagan M. Billakanti
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Industrial Research Limited, Lower Hutt, New Zealand
| | - Akshita Wason
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sabrina Keller
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Juliet A. Gerrard
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Industrial Research Limited, Lower Hutt, New Zealand
| | - Frederick Grant Pearce
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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42
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Atkinson SC, Dogovski C, Downton MT, Pearce FG, Reboul CF, Buckle AM, Gerrard JA, Dobson RCJ, Wagner J, Perugini MA. Crystal, solution and in silico structural studies of dihydrodipicolinate synthase from the common grapevine. PLoS One 2012; 7:e38318. [PMID: 22761676 PMCID: PMC3382604 DOI: 10.1371/journal.pone.0038318] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 05/08/2012] [Indexed: 11/22/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant DHDPS structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608-621). Whilst N. sylvestris DHDPS also forms a homotetramer, the plant enzyme adopts a 'back-to-back' dimer of dimers compared to the 'head-to-head' architecture observed for bacterial DHDPS tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris DHDPS is common to all plant DHDPS enzymes. Here, we describe the structure of DHDPS from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera DHDPS forms a 'back-to-back' homotetramer, consistent with N. sylvestris DHDPS. This study is the first to demonstrate using both crystal and solution state measurements that DHDPS from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study.
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Affiliation(s)
- Sarah C. Atkinson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Con Dogovski
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Matthew T. Downton
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Australia
| | - F. Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Cyril F. Reboul
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - John Wagner
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Australia
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
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Reboul CF, Porebski BT, Griffin MDW, Dobson RCJ, Perugini MA, Gerrard JA, Buckle AM. Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase. PLoS Comput Biol 2012; 8:e1002537. [PMID: 22685390 PMCID: PMC3369909 DOI: 10.1371/journal.pcbi.1002537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 04/16/2012] [Indexed: 11/18/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) is an essential enzyme involved in the lysine biosynthesis pathway. DHDPS from E. coli is a homotetramer consisting of a 'dimer of dimers', with the catalytic residues found at the tight-dimer interface. Crystallographic and biophysical evidence suggest that the dimers associate to stabilise the active site configuration, and mutation of a central dimer-dimer interface residue destabilises the tetramer, thus increasing the flexibility and reducing catalytic efficiency and substrate specificity. This has led to the hypothesis that the tetramer evolved to optimise the dynamics within the tight-dimer. In order to gain insights into DHDPS flexibility and its relationship to quaternary structure and function, we performed comparative Molecular Dynamics simulation studies of native tetrameric and dimeric forms of DHDPS from E. coli and also the native dimeric form from methicillin-resistant Staphylococcus aureus (MRSA). These reveal a striking contrast between the dynamics of tetrameric and dimeric forms. Whereas the E. coli DHDPS tetramer is relatively rigid, both the E. coli and MRSA DHDPS dimers display high flexibility, resulting in monomer reorientation within the dimer and increased flexibility at the tight-dimer interface. The mutant E. coli DHDPS dimer exhibits disorder within its active site with deformation of critical catalytic residues and removal of key hydrogen bonds that render it inactive, whereas the similarly flexible MRSA DHDPS dimer maintains its catalytic geometry and is thus fully functional. Our data support the hypothesis that in both bacterial species optimal activity is achieved by fine tuning protein dynamics in different ways: E. coli DHDPS buttresses together two dimers, whereas MRSA dampens the motion using an extended tight-dimer interface.
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Affiliation(s)
- C. F. Reboul
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - B. T. Porebski
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - M. D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - R. C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Biomolecular Interaction Centre, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M. A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - J. A. Gerrard
- Biomolecular Interaction Centre, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - A. M. Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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Schnell R, Oehlmann W, Sandalova T, Braun Y, Huck C, Maringer M, Singh M, Schneider G. Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion. PLoS One 2012; 7:e31133. [PMID: 22359568 PMCID: PMC3281039 DOI: 10.1371/journal.pone.0031133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/03/2012] [Indexed: 11/19/2022] Open
Abstract
The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 Å resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1ΔdapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.
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Affiliation(s)
- Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Wulf Oehlmann
- LIONEX Diagnostics and Therapeutics, Braunschweig, Germany
| | - Tatyana Sandalova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yvonne Braun
- LIONEX Diagnostics and Therapeutics, Braunschweig, Germany
| | | | | | - Mahavir Singh
- LIONEX Diagnostics and Therapeutics, Braunschweig, Germany
- * E-mail: (MS); (GS)
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MS); (GS)
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45
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Atkinson SC, Dogovski C, Newman J, Dobson RCJ, Perugini MA. Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1537-41. [PMID: 22139160 PMCID: PMC3232133 DOI: 10.1107/s1744309111038395] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/19/2011] [Indexed: 11/11/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of DHDPS from the grapevine Vitis vinifera (Vv-DHDPS). Following in-drop cleavage of the hexahistidine tag, cocrystals of Vv-DHDPS with the substrate pyruvate were grown in 0.1 M Bis-Tris propane pH 8.2, 0.2 M sodium bromide, 20%(w/v) PEG 3350. X-ray diffraction data in space group P1 at a resolution of 2.2 Å are presented. Preliminary diffraction data analysis indicated the presence of eight molecules per asymmetric unit (V(M) = 2.55 Å(3) Da(-1), 52% solvent content). The pending crystal structure of Vv-DHDPS will provide insight into the molecular evolution in quaternary structure of DHDPS enzymes.
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Affiliation(s)
- Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Janet Newman
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Griffin MDW, Billakanti JM, Gerrard JA, Dobson RCJ, Pearce FG. Crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase 2 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1386-90. [PMID: 22102238 PMCID: PMC3212457 DOI: 10.1107/s1744309111033276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/16/2011] [Indexed: 11/10/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) catalyzes the first committed step of the lysine-biosynthetic pathway in plants and bacteria. Since (S)-lysine biosynthesis does not occur in animals, DHDPS is an attractive target for rational antibiotic and herbicide design. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS2 from Arabidopsis thaliana are reported. Diffraction-quality protein crystals belonged to space group P2(1)2(1)2.
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Affiliation(s)
- Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia.
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Lo HF, Su JY, Chen HL, Chen JC, Lin LL. Biophysical studies of an NAD(P)(+)-dependent aldehyde dehydrogenase from Bacillus licheniformis. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:1131-1142. [PMID: 21874381 DOI: 10.1007/s00249-011-0744-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/09/2011] [Indexed: 05/31/2023]
Abstract
Aldehyde dehydrogenase (ALDH) catalyzes the conversion of aldehydes to the corresponding acids by means of an NAD(P)(+)-dependent virtually irreversible reaction. In this investigation, the biophysical properties of a recombinant Bacillus licheniformis ALDH (BlALDH) were characterized in detail by analytical ultracentrifuge (AUC) and various spectroscopic techniques. The oligomeric state of BlALDH in solution was determined to be tetrameric by AUC. Far-UV circular dichroism analysis revealed that the secondary structures of BlALDH were not altered in the presence of acetone and ethanol, whereas SDS had a detrimental effect on the folding of the enzyme. Thermal unfolding of this enzyme was found to be highly irreversible. The native enzyme started to unfold beyond ~0.2 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl](05, N-U), at 0.93 M. BlALDH was active at concentrations of urea below 2 M, but it experienced an irreversible unfolding under 8 M denaturant. Taken together, this study provides a foundation for the future structural investigation of BlALDH, a typical member of ALDH superfamily enzymes.
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Affiliation(s)
- Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Shalu, Taichung City, Taiwan
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Pearce FG, Dobson RCJ, Jameson GB, Perugini MA, Gerrard JA. Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1900-9. [PMID: 21803176 DOI: 10.1016/j.bbapap.2011.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/14/2011] [Accepted: 07/15/2011] [Indexed: 01/15/2023]
Abstract
To gain insights into the role of quaternary structure in the TIM-barrel family of enzymes, we introduced mutations to the DHDPS enzyme of Thermotoga maritima, which we have previously shown to be a stable tetramer in solution. These mutations were aimed at reducing the number of salt bridges at one of the two tetramerization interface of the enzyme, which contains many more interactions than the well characterized equivalent interface of the mesophilic Escherichia coli DHDPS enzyme. The resulting variants had altered quaternary structure, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies confirmed that one variant existed as an independent monomer, but with few changes to the secondary and tertiary structure. Reduction of higher order assembly resulted in a loss of thermal stability, as measured by a variety of methods, and impaired catalytic function. Binding of pyruvate increased the oligomeric status of the variants, with a concomitant increase in thermal stability, suggesting a role for substrate binding in optimizing stable, higher order structures. The results of this work show that the salt bridges located at the tetramerization interface of DHDPS play a significant role in maintaining higher order structures, and demonstrate the importance of quaternary structure in determining protein stability and in the optimization of enzyme catalysis.
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Affiliation(s)
- F Grant Pearce
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Dommaraju SR, Dogovski C, Czabotar PE, Hor L, Smith BJ, Perugini MA. Catalytic mechanism and cofactor preference of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus. Arch Biochem Biophys 2011; 512:167-74. [PMID: 21704017 DOI: 10.1016/j.abb.2011.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 10/18/2022]
Abstract
Given the rapid rise in antibiotic resistance, including methicillin resistance in Staphylococcus aureus (MRSA), there is an urgent need to characterize novel drug targets. Enzymes of the lysine biosynthesis pathway in bacteria are examples of such targets, including dihydrodipicolinate reductase (DHDPR, E.C. 1.3.1.26), which is the product of an essential bacterial gene. DHDPR catalyzes the NAD(P)H-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) in the lysine biosynthesis pathway. We show that MRSA-DHDPR exhibits a unique nucleotide specificity utilizing NADPH (K(m)=12μM) as a cofactor more effectively than NADH (K(m)=26μM). However, the enzyme is inhibited by high concentrations of DHDP when using NADPH as a cofactor, but not with NADH. Isothermal titration calorimetry (ITC) studies reveal that MRSA-DHDPR has ∼20-fold greater binding affinity for NADPH (K(d)=1.5μM) relative to NADH (K(d)=29μM). Kinetic investigations in tandem with ITC studies show that the enzyme follows a compulsory-order ternary complex mechanism; with inhibition by DHDP through the formation of a nonproductive ternary complex with NADP(+). This work describes, for the first time, the catalytic mechanism and cofactor preference of MRSA-DHDPR, and provides insight into rational approaches to inhibiting this valid antimicrobial target.
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Affiliation(s)
- Sudhir R Dommaraju
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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