51
|
Evans G, Schuldt L, Griffin MDW, Devenish SRA, Grant Pearce F, Perugini MA, Dobson RCJ, Jameson GB, Weiss MS, Gerrard JA. A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis. Arch Biochem Biophys 2011; 512:154-9. [PMID: 21672512 DOI: 10.1016/j.abb.2011.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 11/19/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) is a validated antibiotic target for which a new approach to inhibitor design has been proposed: disrupting native tetramer formation by targeting the dimer-dimer interface. In this study, rational design afforded a variant of Mycobacterium tuberculosis, Mtb-DHDPS-A204R, with disrupted quaternary structure. X-ray crystallography (at a resolution of 2.1Å) revealed a dimeric protein with an identical fold and active-site structure to the tetrameric wild-type enzyme. Analytical ultracentrifugation confirmed the dimeric structure in solution, yet the dimeric mutant has similar activity to the wild-type enzyme. Although the affinity for both substrates was somewhat decreased, the high catalytic competency of the enzyme was surprising in the light of previous results showing that dimeric variants of the Escherichia coli and Bacillus anthracis DHDPS enzymes have dramatically reduced activity compared to their wild-type tetrameric counterparts. These results suggest that Mtb-DHDPS-A204R is similar to the natively dimeric enzyme from Staphylococcus aureus, and highlight our incomplete understanding of the role played by oligomerisation in relating protein structure and function.
Collapse
Affiliation(s)
- Genevieve Evans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | | | | | | | | | | | | | | | | |
Collapse
|
52
|
Gorman MA, Uboldi AD, Walsh PJ, Tan KS, Hansen G, Huyton T, Ji H, Curtis J, Kedzierski L, Papenfuss AT, Dogovski C, Perugini MA, Simpson RJ, Handman E, Parker MW. Crystal structure of the Leishmania major MIX protein: a scaffold protein that mediates protein-protein interactions. Protein Sci 2011; 20:1060-8. [PMID: 21465610 PMCID: PMC3104235 DOI: 10.1002/pro.631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/15/2011] [Accepted: 03/22/2011] [Indexed: 01/07/2023]
Abstract
Infection by Leishmania and Trypanosoma causes severe disease and can be fatal. The reduced effectiveness of current treatments is largely due to drug resistance, hence the urgent need to develop new drugs, preferably against novel targets. We have recently identified a mitochondrial membrane-anchored protein, designated MIX, which occurs exclusively in these parasites and is essential for virulence. We have determined the crystal structure of Leishmania major MIX to a resolution of 2.4 Å. MIX forms an all α-helical fold comprising seven α-helices that fold into a single domain. The distribution of helices is similar to a number of scaffold proteins, namely HEAT repeats, 14-3-3, and tetratricopeptide repeat proteins, suggesting that MIX mediates protein-protein interactions. Accordingly, using copurification and mass spectroscopy we were able to identify several proteins that may interact with MIX in vivo. Being parasite specific, MIX is a promising new drug target and, thus, the structure and potential interacting partners provide a basis for structure-guided drug discovery.
Collapse
Affiliation(s)
- Michael A Gorman
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical ResearchVictoria 3065, Australia
| | - Alex D Uboldi
- Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchVictoria 3052, Australia
| | - Peter J Walsh
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical ResearchVictoria 3065, Australia
| | - Kher Shing Tan
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical ResearchVictoria 3065, Australia
| | - Guido Hansen
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical ResearchVictoria 3065, Australia
| | - Trevor Huyton
- The Australia Synchrotron800 Blackburn Road, Victoria 3168, Australia
| | - Hong Ji
- Ludwig Institute for Cancer ResearchVictoria 3050, Australia
| | - Joan Curtis
- Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchVictoria 3052, Australia
| | - Lukasz Kedzierski
- Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchVictoria 3052, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical ResearchVictoria 3052, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoria 3010, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoria 3010, Australia
| | | | - Emanuela Handman
- Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchVictoria 3052, Australia
| | - Michael W Parker
- Biota Structural Biology Laboratory, St. Vincent's Institute of Medical ResearchVictoria 3065, Australia,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoria 3010, Australia,*Correspondence to: Michael W. Parker, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia. E-mail:
| |
Collapse
|
53
|
Dobson RCJ, Girón I, Hudson AO. L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development. PLoS One 2011; 6:e20439. [PMID: 21633707 PMCID: PMC3102117 DOI: 10.1371/journal.pone.0020439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022] Open
Abstract
In some bacterial species and photosynthetic cohorts, including algae, the enzyme
l,l-diaminopimelate aminotransferase
(DapL) (E.C. 2.6.1.83) is involved in the anabolism of the essential amino acid
L-lysine. DapL catalyzes the conversion of
tetrahydrodipicolinate (THDPA) to
l,l-diaminopimelate
(l,l-DAP), in one step bypassing the
DapD, DapC and DapE enzymatic reactions present in the acyl DAP pathways. Here
we present an in vivo and in vitro
characterization of the DapL ortholog from the alga Chlamydomonas
reinhardtii (Cr-DapL). The in
vivo analysis illustrated that the enzyme is able to functionally
complement the E. coli dap auxotrophs and was essential for
plant development in Arabidopsis. In vitro, the enzyme was able
to inter-convert THDPA and l,l-DAP, showing
strong substrate specificity. Cr-DapL was dimeric in both
solution and when crystallized. The structure of Cr-DapL was
solved in its apo form, showing an overall architecture of a
α/β protein with each monomer in the dimer adopting a pyridoxal
phosphate-dependent transferase-like fold in a V-shaped conformation. The active
site comprises residues from both monomers in the dimer and shows some
rearrangement when compared to the apo-DapL structure from
Arabidopsis. Since animals do not possess the enzymatic machinery necessary for
the de novo synthesis of the amino acid
l-lysine, enzymes involved in this pathway are
attractive targets for the development of antibiotics, herbicides and
algaecides.
Collapse
Affiliation(s)
- Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science
and Biotechnology Institute, The University of Melbourne, Parkville, Victoria,
Australia
- Biomolecular Interaction Centre, School of Biological Sciences,
University of Canterbury, Christchurch, New Zealand
- * E-mail: (RCJD); (AOH)
| | - Irma Girón
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
| | - André O. Hudson
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
- * E-mail: (RCJD); (AOH)
| |
Collapse
|
54
|
Biochemical studies and crystal structure determination of dihydrodipicolinate synthase from Pseudomonas aeruginosa. Int J Biol Macromol 2011; 48:779-87. [PMID: 21396954 DOI: 10.1016/j.ijbiomac.2011.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/28/2011] [Accepted: 03/02/2011] [Indexed: 11/20/2022]
Abstract
The intracellular enzyme dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) from Pseudomonas aeruginosa is a potential drug target because it is essential for the growth of bacteria while it is absent in humans. Therefore, in order to design new compounds using structure based approach for inhibiting the function of DHDPS from P. aeruginosa (Ps), we have cloned, characterized biochemically and biophysically and have determined its three-dimensional structure. The gene encoding DHDPS (dapA) was cloned in a vector pET-28c(+) and the recombinant protein was overexpressed in the Escherichia coli host. The K(m) values of the recombinant enzyme estimated for the substrates, pyruvate and (S)-aspartate-β-semialdehyde [(S)-ASA] were found to be 0.90±0.13 mM and 0.17±0.02 mM, respectively. The circular dichroism studies showed that the enzyme adopts a characteristic β/α conformation which is retained up to 65°C. The fluorescence data indicated the presence of exposed tryptophan residues in the enzyme. The three-dimensional structure determination showed that DHDPS forms a homodimer which is stabilized by several hydrogen bonds and van der Waals forces at the interface. The active site formed with residues Thr44, Tyr107 and Tyr133 is found to be stereochemically suitable for catalytic function. It may be noted that Tyr107 of the catalytic triad belongs to the partner molecule in the dimer. The structure of the complex of PsDHDPS with (S)-lysine determined at 2.65 Å resolution revealed the positions of three lysine molecules bound to the protein.
Collapse
|
55
|
Yang JC, Liang WC, Chen YY, Chi MC, Lo HF, Chen HL, Lin LL. Biophysical characterization of Bacillus licheniformis and Escherichia coli γ-glutamyltranspeptidases: A comparative analysis. Int J Biol Macromol 2011; 48:414-22. [PMID: 21238482 DOI: 10.1016/j.ijbiomac.2011.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/22/2010] [Accepted: 01/04/2011] [Indexed: 11/24/2022]
Abstract
The oligomeric states of Bacillus licheniformis and Escherichia coli γ-glutamyltranspeptidases (BlGGT and EcGGT) in solution have been investigated by analytical ultracentrifugation. The results showed that BlGGT has a sedimentation coefficient of 5.12S, which can be transformed into an experimental molecular mass of approximately 62,680Da. The monomeric conformation is conserved in EcGGT. SDS-PAGE analysis and cross-linking studies further proved that the autocatalytically processed BlGGT and EcGGT form a heterodimeric association. Unfolding analyses using circular dichroism and tryptophan emission fluorescence revealed that these two proteins had a different sensitivity towards temperature- and guanidine hydrochloride (GdnHCl)-induced denaturation. BlGGT and EcGGT had a T(m) value of 59.5 and 49.2°C, respectively, and thermal unfolding of both proteins was found to be highly irreversible. Chemical unfolding of BlGGT was independent to the pH value ranging from 5 to 10, whereas the pH environment was found to significantly influence the GdnHCl-induced denaturation of EcGGT. Both enzymes did not reactivate from the completely unfolded states, accessible at 6M GdnHCl. BlGGT was active in the presence of 4M NaCl, whereas the activity of EcGGT was significantly decreased at the high-salt condition. Taken together, these findings suggest that the biophysical properties of the homologous GGTs from two mesophilic sources are quite different.
Collapse
Affiliation(s)
- Jia-Ci Yang
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi County 60004, Taiwan
| | | | | | | | | | | | | |
Collapse
|
56
|
Kingsbury JS, Laue TM. Fluorescence-detected sedimentation in dilute and highly concentrated solutions. Methods Enzymol 2011; 492:283-304. [PMID: 21333796 DOI: 10.1016/b978-0-12-381268-1.00021-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Analytical ultracentrifugation (AUC) is a powerful, first-principles method for characterizing macromolecules in solution. The recent development of fluorescence-detected sedimentation for the AUC (AU-FDS) has extended the sensitivity and selectivity of the instrument which, in turn, has enabled the study of both higher affinity interactions and the sedimentation of one component in complex, concentrated solutions. While still in its infancy, AU-FDS is becoming more widespread as shown by the increasing number of literature reports citing its use. While AU-FDS enables the analysis of systems not amenable to absorbance or interferometric detection, its use is not without limitations. In most cases, preparing samples for AU-FDS analyses requires chemical conjugation with fluorescent dyes, a step that may influence the size or shape of a molecule sufficiently to alter its transport during sedimentation. Careful preparation and characterization of the amount of free dye and the degree and site specificity of labeling is required for robust interpretation of AU-FDS data. In some cases, studies of the effect of labeling on the structure, activity, or association properties of the macromolecule may be warranted. However, these complications are of minor consequence compared to the unique information that can be obtained by AU-FDS. In particular, its ability to provide direct, physical characterization of the thermodynamic behavior of molecules in complex and concentrated solutions makes AU-FDS a powerful technology for understanding the physical underpinnings of living systems.
Collapse
Affiliation(s)
- Jonathan S Kingsbury
- Therapeutic Protein Research, Genzyme Corporation, Framingham, Massachusetts, USA
| | | |
Collapse
|
57
|
Hudson AO, Girón I, Dobson RCJ. Crystallization and preliminary X-ray diffraction analysis of L,L-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:140-3. [PMID: 21206046 PMCID: PMC3079994 DOI: 10.1107/s174430911004844x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/20/2010] [Indexed: 11/10/2022]
Abstract
In the anabolic synthesis of diaminopimelate and lysine in plants and in some bacteria, the enzyme L,L-diaminopimelate aminotransferase (DapL; EC 2.6.1.83) catalyzes the conversion of tetrahydrodipicolinic acid (THDPA) to L,L-diaminopimelate, bypassing the DapD, DapC and DapE enzymatic steps in the bacterial acyl pathways. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapL from the alga Chlamydomonas reinhardtii are presented. Protein crystals were grown in conditions containing 25% (w/v) PEG 3350 and 200 mM lithium sulfate and initially diffracted to ∼1.35 Å resolution. They belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=58.9, b=91.8, c=162.9 Å. The data were processed to 1.55 Å resolution with an Rmerge of 0.081, an Rp.i.m. of 0.044, an Rr.i.m of 0.093 and a VM of 2.28 Å3 Da(-1).
Collapse
Affiliation(s)
- André O. Hudson
- School of Biological and Medical Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Irma Girón
- School of Biological and Medical Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - 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
| |
Collapse
|
58
|
Biophysical Characterization of a Recombinant α-Amylase from Thermophilic Bacillus sp. strain TS-23. Protein J 2010; 29:572-82. [DOI: 10.1007/s10930-010-9287-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
59
|
Mok YF, Ryan TM, Yang S, Hatters DM, Howlett GJ, Griffin MDW. Sedimentation velocity analysis of amyloid oligomers and fibrils using fluorescence detection. Methods 2010; 54:67-75. [PMID: 21055469 DOI: 10.1016/j.ymeth.2010.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 10/21/2010] [Accepted: 10/28/2010] [Indexed: 11/25/2022] Open
Abstract
The assembly of proteins into large fibrillar aggregates, known as amyloid fibrils, is associated with a number of common and debilitating diseases. In some cases, proteins deposit extracellularly, while in others the aggregation is intracellular. A common feature of these diseases is the presence of aggregates of different sizes, including mature fibrils, small oligomeric precursors, and other less well understood structural forms such as amorphous aggregates. These various species possess distinct biochemical, biophysical, and pathological properties. Here, we detail a number of techniques that can be employed to examine amyloid fibrils and oligomers using a fluorescence-detection system (FDS) coupled with the analytical ultracentrifuge. Sedimentation velocity analysis using fluorescence detection is a particularly useful method for resolving the complex heterogeneity present in amyloid systems and can be used to characterize aggregation in exceptional detail. Furthermore, the fluorescence detection module provides a number of particularly attractive features for the analysis of aggregating proteins. It expands the practical range of concentrations of aggregating proteins under study, which is useful for greater insight into the aggregation process. It also enables the assessment of aggregation behavior in complex biological solutions, such as cell lysates, and the assessment of processes that regulate in-cell or extracellular aggregation kinetics. Four methods of fluorescent detection that are compatible with the current generation of FDS instrumentation are described: (1) Detection of soluble amyloid fibrils using a covalently bound fluorophore. (2) Detection of amyloid fibrils using an extrinsic dye that emits fluorescence when bound to fibrils. (3) Detection of fluorescently-labeled lipids and their interaction with oligomeric amyloid intermediates. (4) Detection of green fluorescence protein (GFP) constructs and their interactions within mammalian cell lysates.
Collapse
Affiliation(s)
- Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | |
Collapse
|
60
|
Wubben JM, Dogovski C, Dobson RCJ, Codd R, Gerrard JA, Parker MW, Perugini MA. Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the psychrophile Shewanella benthica. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1511-6. [PMID: 21045309 PMCID: PMC3001662 DOI: 10.1107/s1744309110036791] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 09/14/2010] [Indexed: 11/10/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) is an oligomeric enzyme that catalyzes the first committed step of the lysine-biosynthesis pathway in plants and bacteria, which yields essential building blocks for cell-wall and protein synthesis. DHDPS is therefore of interest to drug-discovery research as well as to studies that probe the importance of quaternary structure to protein function, stability and dynamics. Accordingly, DHDPS from the psychrophilic (cold-dwelling) organism Shewanella benthica (Sb-DHDPS) was cloned, expressed, purified and crystallized. The best crystals of Sb-DHDPS were grown in 200 mM ammonium sulfate, 100 mM bis-tris pH 5.0-6.0, 23-26%(w/v) PEG 3350, 0.02%(w/v) sodium azide and diffracted to beyond 2.5 Å resolution. Processing of diffraction data to 2.5 Å resolution resulted in a unit cell with space group P2(1)2(1)2(1) and dimensions a = 73.1, b = 84.0, c = 143.7 Å. These studies of the first DHDPS enzyme to be characterized from a bacterial psychrophile will provide insight into the molecular evolution of enzyme structure and dynamics.
Collapse
Affiliation(s)
- Jacinta M. Wubben
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Rachel Codd
- School of Medical Sciences (Pharmacology) and Bosch Institute, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
- St Vincents Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| |
Collapse
|
61
|
Kozer N, Henderson C, Bailey MF, Rothacker J, Nice EC, Burgess AW, Clayton AHA. Creation and Biophysical Characterization of a High-Affinity, Monomeric EGF Receptor Ectodomain Using Fluorescent Proteins. Biochemistry 2010; 49:7459-66. [DOI: 10.1021/bi1008134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Noga Kozer
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
- Centre for Microphotonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Christine Henderson
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
- Centre for Microphotonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Michael F. Bailey
- Department of Biochemistry and Molecular Biology, BIO21 Institute, The University of Melbourne, Melbourne, Victoria 3050, Australia
| | - Julie Rothacker
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
| | - Edouard C. Nice
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
| | - Anthony W. Burgess
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
| | - Andrew H. A. Clayton
- Ludwig Institute for Cancer Research, P.O. Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
- Centre for Microphotonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
| |
Collapse
|
62
|
Disruption of quaternary structure in Escherichia coli dihydrodipicolinate synthase (DHDPS) generates a functional monomer that is no longer inhibited by lysine. Arch Biochem Biophys 2010; 503:202-6. [PMID: 20709017 DOI: 10.1016/j.abb.2010.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/07/2010] [Accepted: 08/10/2010] [Indexed: 11/22/2022]
Abstract
Escherichia coli dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a natively homotetrameric enzyme was converted to a monomeric species through the introduction of destabilising interactions at two different subunit interfaces allowing exploration of the roles of the quaternary structure in affecting catalytic competency. The double mutant DHDPS-L197D/Y107W displays gel filtration characteristics consistent with a single non-interacting monomeric species, which was confirmed by sedimentary velocity experiments. This monomer was shown to be catalytically active, but with reduced catalytic efficiency (k(cat)=9.8±0.5s(-1)), displaying 8% of the specific activity of the wild-type enzyme. The Michaelis constants for the substrates pyruvate and for (S)-aspartate semialdehyde increased by an order of magnitude, indicating that quaternary structure plays a significant role in substrate specificity. This monomeric species exhibited an enhanced propensity for aggregation and inactivation, indicating that whilst the oligomerization is not an intrinsic criterion for catalysis, higher oligomeric forms may benefit from both increased catalytic efficiency and diminished aggregation propensity. Furthermore, allosteric inhibition by (S)-lysine was abolished for DHDPS-L197D/Y107W, confirming the importance of the dimeric unit as the minimal functional assembly for efficient (S)-lysine binding.
Collapse
|
63
|
Soares da Costa TP, Muscroft-Taylor AC, Dobson RCJ, Devenish SRA, Jameson GB, Gerrard JA. How essential is the ‘essential’ active-site lysine in dihydrodipicolinate synthase? Biochimie 2010; 92:837-45. [PMID: 20353808 DOI: 10.1016/j.biochi.2010.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/08/2010] [Indexed: 11/15/2022]
Affiliation(s)
- Tatiana P Soares da Costa
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | | | | | | | | |
Collapse
|
64
|
Griffin MD, Dobson RC, Gerrard JA, Perugini MA. Exploring the dihydrodipicolinate synthase tetramer: How resilient is the dimer–dimer interface? Arch Biochem Biophys 2010; 494:58-63. [DOI: 10.1016/j.abb.2009.11.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 11/10/2009] [Accepted: 11/10/2009] [Indexed: 11/15/2022]
|
65
|
Karbassi F, Quiros V, Pancholi V, Kornblatt MJ. Dissociation of the octameric enolase from S. pyogenes--one interface stabilizes another. PLoS One 2010; 5:e8810. [PMID: 20098674 PMCID: PMC2809091 DOI: 10.1371/journal.pone.0008810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 12/20/2009] [Indexed: 11/18/2022] Open
Abstract
Most enolases are homodimers. There are a few that are octamers, with the eight subunits arranged as a tetramer of dimers. These dimers have the same basic fold and same subunit interactions as are found in the dimeric enolases. The dissociation of the octameric enolase from S. pyogenes was examined, using NaClO4, a weak chaotrope, to perturb the quaternary structure. Dissociation was monitored by sedimentation velocity. NaClO4 dissociated the octamer into inactive monomers. There was no indication that dissociation of the octamer into monomers proceeded via formation of significant amounts of dimer or any other intermediate species. Two mutations at the dimer-dimer interface, F137L and E363G, were introduced in order to destabilize the octameric structure. The double mutant was more easily dissociated than was the wild type. Dissociation could also be produced by other salts, including tetramethylammonium chloride (TMACl) or by increasing pH. In all cases, no significant amounts of dimers or other intermediates were formed. Weakening one interface in this protein weakened the other interface as well. Although enolases from most organisms are dimers, the dimeric form of the S. pyogenes enzyme appears to be unstable.
Collapse
Affiliation(s)
- Farhad Karbassi
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Veronica Quiros
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Vijay Pancholi
- Department of Pathology, Ohio State University, Columbus, Ohio, United States of America
| | - Mary J. Kornblatt
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
- * E-mail:
| |
Collapse
|
66
|
Dommaraju S, Gorman MA, Dogovski C, Pearce FG, Gerrard JA, Dobson RCJ, Parker MW, Perugini MA. Cloning, expression and crystallization of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:57-60. [PMID: 20057072 PMCID: PMC2805538 DOI: 10.1107/s1744309109047964] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 11/12/2009] [Indexed: 03/30/2023]
Abstract
Dihydrodipicolinate reductase (DHDPR; EC 1.3.1.26) catalyzes the nucleotide (NADH/NADPH) dependent second step of the lysine-biosynthesis pathway in bacteria and plants. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPR from methicillin-resistant Staphylococcus aureus (MRSA-DHDPR) are presented. The enzyme was crystallized in a number of forms, predominantly with ammonium sulfate as a precipitant, with the best crystal form diffracting to beyond 3.65 A resolution. Crystal structures of the apo form as well as of cofactor (NADPH) bound and inhibitor (2,6-pyridinedicarboxylate) bound forms of MRSA-DHDPR will provide insight into the structure and function of this essential enzyme and valid drug target.
Collapse
Affiliation(s)
- Sudhir Dommaraju
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Victoria, Australia
| | - Michael A. Gorman
- St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Victoria, Australia
| | - F. Grant Pearce
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand
| | - Juliet A. Gerrard
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Victoria, Australia
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Victoria, Australia
- St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Victoria, Australia
- St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| |
Collapse
|
67
|
Sibarani NE, Gorman MA, Dogovski C, Parker MW, Perugini MA. Crystallization of dihydrodipicolinate synthase from a clinical isolate of Streptococcus pneumoniae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 66:32-6. [PMID: 20057065 DOI: 10.1107/s174430910904771x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/11/2009] [Indexed: 11/10/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) catalyzes the rate-limiting step in the (S)-lysine biosynthesis pathway of bacteria and plants. Here, the cloning of the DHDPS gene from a clinical isolate of Streptococcus pneumoniae (OXC141 strain) and the strategy used to express, purify and crystallize the recombinant enzyme are described. Diffracting crystals were grown in high-molecular-weight PEG precipitants using the hanging-drop vapour-diffusion method. The best crystal, from which data were collected, diffracted to beyond 2.0 A resolution. Initially, the crystals were thought to belong to space group P4(2)2(1)2, with unit-cell parameters a = 105.5, b = 105.5, c = 62.4 A. However, the R factors remained high following initial processing of the data. It was subsequently shown that the data set was twinned and it was thus reprocessed in space group P2, resulting in a significant reduction in the R factors. Determination of the structure will provide insight into the design of novel antimicrobial agents targeting this important enzyme from S. pneumoniae.
Collapse
Affiliation(s)
- Natalia E Sibarani
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | |
Collapse
|
68
|
Voss JE, Scally SW, Taylor NL, Atkinson SC, Griffin MDW, Hutton CA, Parker MW, Alderton MR, Gerrard JA, Dobson RCJ, Dogovski C, Perugini MA. Substrate-mediated stabilization of a tetrameric drug target reveals Achilles heel in anthrax. J Biol Chem 2009; 285:5188-95. [PMID: 19948665 DOI: 10.1074/jbc.m109.038166] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus anthracis is a gram-positive spore-forming bacterium that causes anthrax. With the increased threat of anthrax in biowarfare, there is an urgent need to characterize new antimicrobial targets from B. anthracis. One such target is dihydrodipicolinate synthase (DHDPS), which catalyzes the committed step in the pathway yielding meso-diaminopimelate and lysine. In this study, we employed CD spectroscopy to demonstrate that the thermostability of DHDPS from B. anthracis (Ba-DHDPS) is significantly enhanced in the presence of the substrate, pyruvate. Analytical ultracentrifugation studies show that the tetramer-dimer dissociation constant of the enzyme is 3-fold tighter in the presence of pyruvate compared with the apo form. To examine the significance of this substrate-mediated stabilization phenomenon, a dimeric mutant of Ba-DHDPS (L170E/G191E) was generated and shown to have markedly reduced activity compared with the wild-type tetramer. This demonstrates that the substrate, pyruvate, stabilizes the active form of the enzyme. We next determined the high resolution (2.15 A) crystal structure of Ba-DHDPS in complex with pyruvate (3HIJ) and compared this to the apo structure (1XL9). Structural analyses show that there is a significant (91 A(2)) increase in buried surface area at the tetramerization interface of the pyruvate-bound structure. This study describes a new mechanism for stabilization of the active oligomeric form of an antibiotic target from B. anthracis and reveals an "Achilles heel" that can be exploited in structure-based drug design.
Collapse
Affiliation(s)
- Jarrod E Voss
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
69
|
Devenish SR, Gerrard JA. The quaternary structure of Escherichia coli N-acetylneuraminate lyase is essential for functional expression. Biochem Biophys Res Commun 2009; 388:107-11. [DOI: 10.1016/j.bbrc.2009.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 07/24/2009] [Indexed: 12/19/2022]
|
70
|
Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1510-6. [DOI: 10.1016/j.bbapap.2009.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/05/2009] [Accepted: 06/25/2009] [Indexed: 11/20/2022]
|
71
|
Bailey MF, Angley LM, Perugini MA. Methods for sample labeling and meniscus determination in the fluorescence-detected analytical ultracentrifuge. Anal Biochem 2009; 390:218-20. [PMID: 19348779 DOI: 10.1016/j.ab.2009.03.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 03/30/2009] [Accepted: 03/31/2009] [Indexed: 11/19/2022]
Abstract
The fluorescence detection system for the analytical ultracentrifuge (AU-FDS) enables the measurement of hydrodynamic properties and interactions of biomolecules at subnanomolar concentrations. In this study, we describe methods for (i) preparing and purifying fluorescently labeled biomolecules and (ii) determining the meniscus position in the AU-FDS using BODIPY 493/503 fluorescent dye suspended in light oil. We subsequently use these methods to measure the interaction of DNA with Escherichia coli Klenow fragment (KF) and show that KF binds matched DNA to form 1:1 and 2:1 (protein/DNA) complexes with dissociation constants of 4.2 and 22 nM, respectively.
Collapse
Affiliation(s)
- Michael F Bailey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | |
Collapse
|
72
|
Atkinson SC, Dobson RCJ, Newman JM, Gorman MA, Dogovski C, Parker MW, Perugini MA. Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:253-5. [PMID: 19255476 PMCID: PMC2650466 DOI: 10.1107/s1744309108039018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 11/20/2008] [Indexed: 11/10/2022]
Abstract
In this paper, the crystallization and preliminary X-ray diffraction analysis to near-atomic resolution of DHDPS from Clostridium botulinum crystallized in the presence of its substrate pyruvate are presented. The enzyme crystallized in a number of forms using a variety of PEG precipitants, with the best crystal diffracting to 1.2 A resolution and belonging to space group C2, in contrast to the unbound form, which had trigonal symmetry. The unit-cell parameters were a = 143.4, b = 54.8, c = 94.3 A, beta = 126.3 degrees . The crystal volume per protein weight (V(M)) was 2.3 A(3) Da(-1) (based on the presence of two monomers in the asymmetric unit), with an estimated solvent content of 46%. The high-resolution structure of the pyruvate-bound form of C. botulinum DHDPS will provide insight into the function and stability of this essential bacterial enzyme.
Collapse
Affiliation(s)
- Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Janet M. Newman
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Michael A. Gorman
- St Vincents Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010, Australia
- St Vincents Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010, Australia
| |
Collapse
|
73
|
Devenish SRA, Huisman FHA, Parker EJ, Hadfield AT, Gerrard JA. Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1168-74. [PMID: 19236959 DOI: 10.1016/j.bbapap.2009.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 01/22/2009] [Accepted: 02/05/2009] [Indexed: 11/16/2022]
Abstract
Neisseria meningitidis is an obligate commensal bacterium of humans, and also an important human pathogen. To facilitate future drug studies, we report here the biochemical and structural characterisation of a key enzyme in (S)-lysine biosynthesis, dihydrodipicolinate synthase (DHDPS), from N. meningitidis (NmeDHDPS). X-ray crystallography revealed only minor structural differences between NmeDHDPS and the enzyme from E. coli at the active and allosteric effector sites. The catalytic capabilities of NmeDHDPS are similar to those of the enzyme from E. coli, but intriguingly NmeDHDPS is subject to substrate inhibition by high concentrations of the second substrate, (S)-aspartate semialdehyde, and is also significantly more sensitive to feedback inhibition by (S)-lysine. This heightened sensitivity to inhibition at both active and allosteric sites suggests that it may be possible to target DHDPS from N. meningitidis for antibiotic development.
Collapse
Affiliation(s)
- Sean R A Devenish
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | | | | | | | | |
Collapse
|
74
|
Guo BBB, Devenish SRA, Dobson RCJ, Muscroft-Taylor AC, Gerrard JA. The C-terminal domain of Escherichia coli dihydrodipicolinate synthase (DHDPS) is essential for maintenance of quaternary structure and efficient catalysis. Biochem Biophys Res Commun 2009; 380:802-6. [PMID: 19338756 DOI: 10.1016/j.bbrc.2009.01.169] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the biosynthesis of (S)-lysine, an essential constituent of bacterial cell walls. Escherichia coli DHDPS is homotetrameric, and each monomer contains an N-terminal (alpha/beta)(8)-barrel, responsible for catalysis and regulation, and three C-terminal alpha-helices, the function of which is unknown. This study investigated the C-terminal domain of E. coli DHDPS by characterising a C-terminal truncated DHDPS (DHDPS-H225*). DHDPS-H225* was unable to complement an (S)-lysine auxotroph, and showed significantly reduced solubility, stability, and maximum catalytic activity (k(cat)=1.20+/-0.01 s(-1)), which was only 1.6% of wild type E. coli DHDPS (DHDPS-WT). The affinity of DHDPS-H225* for substrates and the feedback inhibitor, (S)-lysine, remained comparable to DHDPS-WT. These changes were accompanied by disruption in the quaternary structure, which has previously been shown to be essential for efficient catalysis in this enzyme.
Collapse
Affiliation(s)
- Belinda B B Guo
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Ilam, Christchurch, Canterbury 4800, New Zealand
| | | | | | | | | |
Collapse
|
75
|
Voss JE, Scally SW, Taylor NL, Dogovski C, Alderton MR, Hutton CA, Gerrard JA, Parker MW, Dobson RCJ, Perugini MA. Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:188-91. [PMID: 19194017 PMCID: PMC2635873 DOI: 10.1107/s1744309109000670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 01/07/2009] [Indexed: 11/11/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the lysine-biosynthesis pathway in bacteria, plants and some fungi. In this study, the expression of DHDPS from Bacillus anthracis (Ba-DHDPS) and the purification of the recombinant enzyme in the absence and presence of the substrate pyruvate are described. It is shown that DHDPS from B. anthracis purified in the presence of pyruvate yields greater amounts of recombinant enzyme with more than 20-fold greater specific activity compared with the enzyme purified in the absence of substrate. It was therefore sought to crystallize Ba-DHDPS in the presence of the substrate. Pyruvate was soaked into crystals of Ba-DHDPS prepared in 0.2 M sodium fluoride, 20%(w/v) PEG 3350 and 0.1 M bis-tris propane pH 8.0. Preliminary X-ray diffraction data of the recombinant enzyme soaked with pyruvate at a resolution of 2.15 A are presented. The pending crystal structure of the pyruvate-bound form of Ba-DHDPS will provide insight into the function and stability of this essential bacterial enzyme.
Collapse
Affiliation(s)
- Jarrod E Voss
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
76
|
Devenish SRA, Gerrard JA. The role of quaternary structure in (β/α)8-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships? Org Biomol Chem 2009; 7:833-9. [DOI: 10.1039/b818251p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
77
|
Kroe RR, Laue TM. NUTS and BOLTS: applications of fluorescence-detected sedimentation. Anal Biochem 2008; 390:1-13. [PMID: 19103145 DOI: 10.1016/j.ab.2008.11.033] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 11/15/2008] [Accepted: 11/21/2008] [Indexed: 11/24/2022]
Abstract
Analytical ultracentrifugation is a widely used method for characterizing the solution behavior of macromolecules. However, the two commonly used detectors, absorbance and interference, impose some fundamental restrictions on the concentrations and complexity of the solutions that can be analyzed. The recent addition of a fluorescence detector for the XL-I analytical ultracentrifuge (AU-FDS) enables two different types of sedimentation experiments. First, the AU-FDS can detect picomolar concentrations of labeled solutes, allowing the characterization of very dilute solutions of macromolecules, applications we call normal use tracer sedimentation (NUTS). The great sensitivity of NUTS analysis allows the characterization of small quantities of materials and high-affinity interactions. Second, the AU-FDS allows characterization of trace quantities of labeled molecules in solutions containing high concentrations and complex mixtures of unlabeled molecules, applications we call biological on-line tracer sedimentation (BOLTS). The discrimination of BOLTS enables the size distribution of a labeled macromolecule to be determined in biological milieus such as cell lysates and serum. Examples that embody features of both NUTS and BOLTS applications are presented along with our observations on these applications.
Collapse
Affiliation(s)
- Rachel R Kroe
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA.
| | | |
Collapse
|
78
|
Pearce FG, Dobson RCJ, Weber A, Lane LA, McCammon MG, Squire MA, Perugini MA, Jameson GB, Robinson CV, Gerrard JA. Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme. Biochemistry 2008; 47:12108-17. [PMID: 18937497 DOI: 10.1021/bi801094t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) is a tetrameric enzyme that is the first enzyme unique to the ( S)-lysine biosynthetic pathway in plants and bacteria. Previous studies have looked at the important role of Tyr107, an amino acid residue located at the tight-dimer interface between two monomers, in participating in a catalytic triad of residues during catalysis. In this study, we examine the importance of this residue in determining the quaternary structure of the DHDPS enzyme. The Tyr107 residue was mutated to tryptophan, and structural, biophysical, and kinetic studies were carried out on the mutant enzyme. These revealed that while the solid-state structure of the mutant enzyme was largely unchanged, as judged by X-ray crystallography, it exists as a mixture of primarily monomer and tetramer in solution, as determined by analytical ultracentrifugation, size-exclusion chromatography, and mass spectrometry. The catalytic ability of the DHDPS enzyme was reduced by the mutation, which also allowed the adventitious binding of alpha-ketoglutarate to the active site. A reduction in the apparent melting temperature of the mutant enzyme was observed. Thus, the tetrameric quaternary structure of DHDPS is critical to controlling specificity, heat stability, and intrinsic activity.
Collapse
Affiliation(s)
- F Grant Pearce
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand
| | | | | | | | | | | | | | | | | | | |
Collapse
|
79
|
Dobson RCJ, Griffin MDW, Devenish SRA, Pearce FG, Hutton CA, Gerrard JA, Jameson GB, Perugini MA. Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. Protein Sci 2008; 17:2080-90. [PMID: 18787203 DOI: 10.1110/ps.037440.108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.
Collapse
Affiliation(s)
- Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.
| | | | | | | | | | | | | | | |
Collapse
|