151
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Chongdar N, Dasgupta S, Datta AB, Basu G. Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase from Escherichia coli. Acta Crystallogr F Struct Biol Commun 2014; 70:922-7. [PMID: 25005090 PMCID: PMC4089533 DOI: 10.1107/s2053230x14010723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/09/2014] [Indexed: 01/02/2023] Open
Abstract
The nature of interaction between glutamyl-tRNA synthetase (GluRS) and its tRNA substrate is unique in bacteria in that many bacterial GluRS are capable of recognizing two tRNA substrates: tRNAGlu and tRNAGln. To properly understand this distinctive GluRS-tRNA interaction it is important to pursue detailed structure-function studies; however, because of the fact that tRNA-GluRS interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation studies must also be phylum-specific. GluRS from Thermus thermophilus and Escherichia coli, which belong to evolutionarily distant phyla, are the biochemically best characterized. Of these, only the structure of T. thermophilus GluRS is available. To fully unravel the subtleties of tRNAGlu-GluRS interaction in E. coli, a model bacterium that can also be pathogenic, determination of the E. coli GluRS structure is essential. However, previous attempts have failed to crystallize E. coli GluRS. By mapping crystal contacts of a homologous GluRS onto the E. coli GluRS sequence, two surface residues were identified that might have been hindering crystallization attempts. Accordingly, these two residues were mutated and crystallization of the double mutant was attempted. Here, the design, expression, purification and crystallization of an engineered E. coli GluRS in which two surface residues were mutated to optimize crystal contacts are reported.
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Affiliation(s)
- Nipa Chongdar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700 054, India
| | - Saumya Dasgupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700 054, India
| | - Ajit Bikram Datta
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700 054, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700 054, India
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152
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Luft JR, Newman J, Snell EH. Crystallization screening: the influence of history on current practice. Acta Crystallogr F Struct Biol Commun 2014; 70:835-53. [PMID: 25005076 PMCID: PMC4089519 DOI: 10.1107/s2053230x1401262x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/30/2014] [Indexed: 11/17/2022] Open
Abstract
While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.
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Affiliation(s)
- Joseph R. Luft
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Janet Newman
- CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, SUNY Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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153
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154
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Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure 2014; 22:949-60. [PMID: 24909784 PMCID: PMC4087270 DOI: 10.1016/j.str.2014.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/24/2014] [Accepted: 04/29/2014] [Indexed: 01/30/2023]
Abstract
Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
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Affiliation(s)
- Christopher N Hoyland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christine Aldridge
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Robert M Cleverley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marie-Clémence Duchêne
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - George Minasov
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Olena Onopriyenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Karzan Sidiq
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Peter J Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Wayne F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID)
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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155
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Harper S, Gratton HE, Cornaciu I, Oberer M, Scott D, Emsley J, Dreveny I. Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains. Biochemistry 2014; 53:2966-78. [PMID: 24724799 PMCID: PMC4020902 DOI: 10.1021/bi500116x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/31/2014] [Indexed: 12/17/2022]
Abstract
The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.
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Affiliation(s)
- Stephen Harper
- Centre for Biomolecular Sciences, University of Nottingham, University
Park Campus, Nottingham, NG7 2RD, United Kingdom
| | - Hayley E. Gratton
- Centre for Biomolecular Sciences, University of Nottingham, University
Park Campus, Nottingham, NG7 2RD, United Kingdom
| | - Irina Cornaciu
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50/3, A-8010 Graz, Austria
| | - Monika Oberer
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße
50/3, A-8010 Graz, Austria
| | - David
J. Scott
- School
of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom
| | - Jonas Emsley
- Centre for Biomolecular Sciences, University of Nottingham, University
Park Campus, Nottingham, NG7 2RD, United Kingdom
| | - Ingrid Dreveny
- Centre for Biomolecular Sciences, University of Nottingham, University
Park Campus, Nottingham, NG7 2RD, United Kingdom
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156
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Skråmo S, Hersleth HP, Hammerstad M, Andersson KK, Røhr ÅK. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:777-80. [PMID: 24915092 DOI: 10.1107/s2053230x14008334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/13/2014] [Indexed: 11/10/2022]
Abstract
Ferredoxin/flavodoxin-NADP(H) oxidoreductases (FNRs) are key enzymes involved in catalysing electron transfer between ferredoxins/flavodoxins and NAD(P)H/NAD(P)+. In Bacillus cereus there are three genes that may encode FNRs, and the Bc0385 FNR has been cloned, overexpressed, purified and successfully crystallized in its NADPH/NADP+-free form. Diffraction data have been collected to 2.5 Å resolution from crystals belonging to the orthorhombic space group P2₁2₁2, with unit-cell parameters a=57.2, b=164.3, c=95.0 Å, containing two FNR molecules in the asymmetric unit. The structure of the Bc0385 FNR has been solved by molecular replacement, and is a member of the homodimeric thioredoxin reductase-like class of FNRs.
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Affiliation(s)
- Silje Skråmo
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - K Kristoffer Andersson
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund K Røhr
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
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157
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Wennman A, Oliw EH, Karkehabadi S. Crystallization and preliminary crystallographic analysis of manganese lipoxygenase. Acta Crystallogr F Struct Biol Commun 2014; 70:522-5. [PMID: 24699754 PMCID: PMC3976078 DOI: 10.1107/s2053230x14005548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/11/2014] [Indexed: 11/10/2022] Open
Abstract
Lipoxygenases constitute a family of nonhaem metal enzymes with catalytic iron or, occasionally, catalytic manganese. Lipoxygenases oxidize polyunsaturated fatty acids with position specificity and stereospecificity to hydroperoxides, which contribute to inflammation and the development of cancer. Little is known about the structural differences between lipoxygenases with Fe or Mn and the metal-selection mechanism. A Pichia pastoris expression system was used for the production of the manganese lipoxygenase of the take-all fungus of wheat, Gaeumannomyces graminis. The active enzyme was treated with α-mannosidase, purified to apparent homogeneity and subjected to crystal screening and X-ray diffraction. The crystals diffracted to 2.6 Å resolution and belonged to space group C2, with unit-cell parameters a = 226.6, b = 50.6, c = 177.92 Å, β = 91.70°.
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Affiliation(s)
- Anneli Wennman
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Ernst H. Oliw
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
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158
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Lagautriere T, Bashiri G, Paterson NG, Berney M, Cook GM, Baker EN. Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies. ACTA ACUST UNITED AC 2014; 70:968-80. [PMID: 24699642 DOI: 10.1107/s1399004713034391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 12/20/2013] [Indexed: 11/10/2022]
Abstract
The proline-utilization pathway in Mycobacterium tuberculosis (Mtb) has recently been identified as an important factor in Mtb persistence in vivo, suggesting that this pathway could be a valuable therapeutic target against tuberculosis (TB). In Mtb, two distinct enzymes perform the conversion of proline into glutamate: the first step is the oxidation of proline into Δ(1)-pyrroline-5-carboxylic acid (P5C) by the flavoenzyme proline dehydrogenase (PruB), and the second reaction involves converting the tautomeric form of P5C (glutamate-γ-semialdehyde) into glutamate using the NAD(+)-dependent Δ(1)-pyrroline-5-carboxylic dehydrogenase (PruA). Here, the three-dimensional structures of Mtb-PruA, determined by X-ray crystallography, in the apo state and in complex with NAD(+) are described at 2.5 and 2.1 Å resolution, respectively. The structure reveals a conserved NAD(+)-binding mode, common to other related enzymes. Species-specific conformational differences in the active site, however, linked to changes in the dimer interface, suggest possibilities for selective inhibition of Mtb-PruA despite its reasonably high sequence identity to other PruA enzymes. Using recombinant PruA and PruB, the proline-utilization pathway in Mtb has also been reconstituted in vitro. Functional validation using a novel NMR approach has demonstrated that the PruA and PruB enzymes are together sufficient to convert proline to glutamate, the first such demonstration for monofunctional proline-utilization enzymes.
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Affiliation(s)
- Thomas Lagautriere
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Ghader Bashiri
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Neil G Paterson
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Michael Berney
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Edward N Baker
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
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159
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Structure of the pseudokinase domain of BIR2, a regulator of BAK1-mediated immune signaling in Arabidopsis. J Struct Biol 2014; 186:112-21. [PMID: 24556575 DOI: 10.1016/j.jsb.2014.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 01/01/2023]
Abstract
The BAK1-interacting receptor-like kinase 2 (BIR2) belongs to the large family of leucine-rich repeat receptor-like kinases (LRR-RLKs) that mediate development and innate immunity in plants and form a monophyletic gene family with the Drosophila Pelle and human interleukin-1 receptor-associated kinases (IRAK). BIR2 is a negative regulator of BAK1-mediated defense mechanisms and cell death responses, yet key residues that are typically required for kinase activity are not present in the BIR2 kinase domain. We have determined the crystal structure of the BIR2 cytosolic domain and show that its nucleotide binding site is occluded. NMR spectroscopy confirmed that neither wild type nor phosphorylation-mimicking mutants of BIR2 bind ATP-analogues in solution, suggesting that BIR2 is a genuine enzymatically inactive pseudokinase. BIR2 is, however, phosphorylated by its target of regulation, BAK1. Using nano LC-MS/MS analysis for site-specific analysis of phosphorylation, we found a high density of BAK1-transphosphorylation sites in the BIR2 juxta membrane domain, a region previously implicated in regulation of RLKs. Our findings provide a structural basis to better understand signaling through kinase-dead domains that are predicted to account for 20% of all Arabidopsis RLKs and 10% of all human kinases.
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160
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McCaughey LC, Grinter R, Josts I, Roszak AW, Waløen KI, Cogdell RJ, Milner J, Evans T, Kelly S, Tucker NP, Byron O, Smith B, Walker D. Lectin-like bacteriocins from Pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor. PLoS Pathog 2014; 10:e1003898. [PMID: 24516380 PMCID: PMC3916391 DOI: 10.1371/journal.ppat.1003898] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/10/2013] [Indexed: 11/24/2022] Open
Abstract
Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins. Due to rapidly increasing rates of antibiotic resistance observed among Gram-negative pathogens, such as Pseudomonas aeruginosa, there is an urgent requirement for novel approaches to the treatment of bacterial infections. Lectin-like bacteriocins are highly potent protein antibiotics that display an unusual ability to kill a select group of bacteria within a specific genus. In this work, we show how the lectin-like protein antibiotic, pyocin L1, can kill Pseudomonas aeruginosa with extraordinary potency through specific binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide. The CPA is predominantly a homopolymer of the sugar d-rhamnose that although generally rare in nature is found frequently as a component of the lipopolysaccharide of members of the genus Pseudomonas. The targeting of d-rhamnose containing polysaccharides by pyocin L1 and a related lectin-like protein antibiotic, putidacin L1, explains the unusual genus- specific killing activity of the lectin-like bacteriocins. As we learn more about the link between changes to the microbiome and a range of chronic diseases there is a growing realisation that the ability to target specific bacterial pathogens while maintaining the normal gut flora is a desirable property for next generation antibiotics.
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Affiliation(s)
- Laura C. McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Aleksander W. Roszak
- WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kai I. Waløen
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joel Milner
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sharon Kelly
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute for Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Smith
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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161
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Łyskowski A, Gruber C, Steinkellner G, Schürmann M, Schwab H, Gruber K, Steiner K. Crystal structure of an (R)-selective ω-transaminase from Aspergillus terreus. PLoS One 2014; 9:e87350. [PMID: 24498081 PMCID: PMC3907554 DOI: 10.1371/journal.pone.0087350] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/19/2013] [Indexed: 11/18/2022] Open
Abstract
Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5′-phosphate (PLP) as cofactor. In nature, (S)-selective amine transaminases are more abundant than the (R)-selective enzymes, and therefore more information concerning their structures is available. Here, we present the crystal structure of an (R)-ω-transaminase from Aspergillus terreus determined by X-ray crystallography at a resolution of 1.6 Å. The structure of the protein is a homodimer that displays the typical class IV fold of PLP-dependent aminotransferases. The PLP-cofactor observed in the structure is present in two states (i) covalently bound to the active site lysine (the internal aldimine form) and (ii) as substrate/product adduct (the external aldimine form) and free lysine. Docking studies revealed that (R)-transaminases follow a dual binding mode, in which the large binding pocket can harbour the bulky substituent of the amine or ketone substrate and the α-carboxylate of pyruvate or amino acids, and the small binding pocket accommodates the smaller substituent.
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Affiliation(s)
| | | | | | | | - Helmut Schwab
- ACIB GmbH, c/o TU Graz, Graz, Austria
- Institute of Molecular Biotechnology, TU Graz, Graz, Austria
| | - Karl Gruber
- ACIB GmbH, c/o TU Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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162
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Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments. ACTA ACUST UNITED AC 2014; 15:13-24. [PMID: 24452510 DOI: 10.1007/s10969-014-9171-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.
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163
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Fairhead M, Krndija D, Lowe ED, Howarth M. Plug-and-play pairing via defined divalent streptavidins. J Mol Biol 2014; 426:199-214. [PMID: 24056174 PMCID: PMC4047826 DOI: 10.1016/j.jmb.2013.09.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022]
Abstract
Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Denis Krndija
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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164
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Niemann V, Koch-Singenstreu M, Neu A, Nilkens S, Götz F, Unden G, Stehle T. The NreA protein functions as a nitrate receptor in the staphylococcal nitrate regulation system. J Mol Biol 2013; 426:1539-53. [PMID: 24389349 DOI: 10.1016/j.jmb.2013.12.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 02/04/2023]
Abstract
Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35Å resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22μM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.
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Affiliation(s)
- Volker Niemann
- Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany
| | - Mareike Koch-Singenstreu
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - Ancilla Neu
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Stephanie Nilkens
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - Friedrich Götz
- Interfaculty Institute of Microbiology and Infection Medicine, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Gottfried Unden
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany.
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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165
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Yu X, Zocher G, Xie X, Liebhold M, Schütz S, Stehle T, Li SM. Catalytic mechanism of stereospecific formation of cis-configured prenylated pyrroloindoline diketopiperazines by indole prenyltransferases. ACTA ACUST UNITED AC 2013; 20:1492-501. [PMID: 24239009 DOI: 10.1016/j.chembiol.2013.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/19/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
Abstract
Indole prenyltransferases AnaPT, CdpC3PT, and CdpNPT are known to catalyze the formation of prenylated pyrroloindoline diketopiperazines from tryptophan-containing cyclic dipeptides in one-step reactions. In this study, we investigated the different stereoselectivities of these enzymes toward all the stereoisomers of cyclo-Trp-Ala and cyclo-Trp-Pro. The stereoselectivities of AnaPT and CdpC3PT mainly depend on the configuration of the tryptophanyl moiety in the substrates, and they usually introduce the prenyl moiety from the opposite sides. CdpNPT showed lower stereoselectivity, and the structure of the second amino acid moiety in the substrates is important for the stereospecificity in its enzyme catalysis. Moreover, we determined the crystal structure of AnaPT in complex with thiolodiphosphate and compared it with the known structures of CdpNPT. Our results clearly revealed the presence of an indole binding mode that has so far not been characterized.
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Affiliation(s)
- Xia Yu
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Georg Zocher
- Interfakultäres Institut für Biochemie, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Mike Liebhold
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Stefan Schütz
- Interfakultäres Institut für Biochemie, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany.
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg 35037, Germany.
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166
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Ruane KM, Lloyd AJ, Fülöp V, Dowson CG, Barreteau H, Boniface A, Dementin S, Blanot D, Mengin-Lecreulx D, Gobec S, Dessen A, Roper DI. Specificity determinants for lysine incorporation in Staphylococcus aureus peptidoglycan as revealed by the structure of a MurE enzyme ternary complex. J Biol Chem 2013; 288:33439-48. [PMID: 24064214 PMCID: PMC3829189 DOI: 10.1074/jbc.m113.508135] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of the peptidoglycan stem pentapeptide requires the insertion of both l and d amino acids by the ATP-dependent ligase enzymes MurC, -D, -E, and -F. The stereochemical control of the third position amino acid in the pentapeptide is crucial to maintain the fidelity of later biosynthetic steps contributing to cell morphology, antibiotic resistance, and pathogenesis. Here we determined the x-ray crystal structure of Staphylococcus aureus MurE UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-2,6-diaminopimelate ligase (MurE) (E.C. 6.3.2.7) at 1.8 Å resolution in the presence of ADP and the reaction product, UDP-MurNAc-l-Ala-γ-d-Glu-l-Lys. This structure provides for the first time a molecular understanding of how this Gram-positive enzyme discriminates between l-lysine and d,l-diaminopimelic acid, the predominant amino acid that replaces l-lysine in Gram-negative peptidoglycan. Despite the presence of a consensus sequence previously implicated in the selection of the third position residue in the stem pentapeptide in S. aureus MurE, the structure shows that only part of this sequence is involved in the selection of l-lysine. Instead, other parts of the protein contribute substrate-selecting residues, resulting in a lysine-binding pocket based on charge characteristics. Despite the absolute specificity for l-lysine, S. aureus MurE binds this substrate relatively poorly. In vivo analysis and metabolomic data reveal that this is compensated for by high cytoplasmic l-lysine concentrations. Therefore, both metabolic and structural constraints maintain the structural integrity of the staphylococcal peptidoglycan. This study provides a novel focus for S. aureus-directed antimicrobials based on dual targeting of essential amino acid biogenesis and its linkage to cell wall assembly.
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Affiliation(s)
- Karen M Ruane
- From the School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, United Kingdom
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167
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Hajnal I, Lyskowski A, Hanefeld U, Gruber K, Schwab H, Steiner K. Biochemical and structural characterization of a novel bacterial manganese-dependent hydroxynitrile lyase. FEBS J 2013; 280:5815-28. [PMID: 23981508 DOI: 10.1111/febs.12501] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
Hydroxynitrile lyases (HNLs), which catalyse the decomposition of cyanohydrins, are found mainly in plants. In vitro, they are able to catalyse the synthesis of enantiopure cyanohydrins, which are versatile building blocks in the chemical industry. Recently, HNLs have also been discovered in bacteria. Here, we report on the detailed biochemical and structural characterization of a hydroxynitrile lyase from Granulicella tundricola (GtHNL), which was successfully heterologously expressed in Escherichia coli. The crystal structure was solved at a crystallographic resolution of 2.5 Å and exhibits a cupin fold. As GtHNL does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs, cupins represent a new class of HNLs. GtHNL is metal-dependent, as confirmed by inductively coupled plasma/optical emission spectroscopy, and in the crystal structure, manganese is bound to three histidine and one glutamine residue. GtHNL displayed a specific activity of 1.74 U·mg(-1) at pH 6 with (R)-mandelonitrile, and synthesized (R)-mandelonitrile with 90% enantiomeric excess at 80% conversion using 0.5 m benzaldehyde in a biphasic reaction system with methyl tertiary butyl ether.
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Affiliation(s)
- Ivan Hajnal
- Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria; Gebouw voor Scheikunde, Technische Universiteit Delft, The Netherlands
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168
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Mevissen T, Hospenthal M, Geurink P, Elliott P, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund S, Ovaa H, Komander D. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis. Cell 2013; 154:169-84. [PMID: 23827681 PMCID: PMC3705208 DOI: 10.1016/j.cell.2013.05.046] [Citation(s) in RCA: 440] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 05/02/2013] [Accepted: 05/28/2013] [Indexed: 11/23/2022]
Abstract
Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates. The 16 human OTU DUBs cleave distinct sets of ubiquitin chain types Five crystal structures of three human OTU DUBs reveal uncharacterized Ub-binding sites We reveal four distinct mechanisms of linkage specificity in OTU DUBs OTU DUBs can be used to identify the linkage types on a ubiquitinated substrate
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Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, D-14195 Berlin, Germany
| | - Manuela K. Hospenthal
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Paul P. Geurink
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paul R. Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Masato Akutsu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Nadia Arnaudo
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Reggy Ekkebus
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yogesh Kulathu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Tobias Wauer
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Farid El Oualid
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Stefan M.V. Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Corresponding author
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169
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Gorrec F. The current approach to initial crystallization screening of proteins is under-sampled. J Appl Crystallogr 2013; 46:795-797. [PMID: 23682195 PMCID: PMC3654315 DOI: 10.1107/s0021889813008030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/23/2013] [Indexed: 11/20/2022] Open
Abstract
Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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170
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Byrne RT, Whelan F, Aller P, Bird LE, Dowle A, Lobley CMC, Reddivari Y, Nettleship JE, Owens RJ, Antson AA, Waterman DG. S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1090-8. [PMID: 23695253 PMCID: PMC3663124 DOI: 10.1107/s0907444913004939] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 02/20/2013] [Indexed: 02/02/2023]
Abstract
The putative methyltransferase CmoA is involved in the nucleoside modification of transfer RNA. X-ray crystallography and mass spectrometry are used to show that it contains a novel SAM derivative, S-adenosyl-S-carboxymethyl-l-homocysteine, in which the donor methyl group is replaced by a carboxymethyl group. Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo5U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo5U and was annotated as an S-adenosyl-l-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel cofactor, S-adenosyl-S-carboxymethyl-l-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-ray structure, PDB entry 1im8, suggests that the active site contains SCM-SAH and not SAM.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, England
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171
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Pryor EE, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. Structure of the integral membrane protein CAAX protease Ste24p. Science 2013; 339:1600-4. [PMID: 23539602 DOI: 10.1126/science.1232048] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.
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172
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CENP-T provides a structural platform for outer kinetochore assembly. EMBO J 2013; 32:424-36. [PMID: 23334297 DOI: 10.1038/emboj.2012.348] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/14/2012] [Indexed: 11/09/2022] Open
Abstract
The kinetochore forms a dynamic interface with microtubules from the mitotic spindle during mitosis. The Ndc80 complex acts as the key microtubule-binding complex at kinetochores. However, it is unclear how the Ndc80 complex associates with the inner kinetochore proteins that assemble upon centromeric chromatin. Here, based on a high-resolution structural analysis, we demonstrate that the N-terminal region of vertebrate CENP-T interacts with the 'RWD' domain in the Spc24/25 portion of the Ndc80 complex. Phosphorylation of CENP-T strengthens a cryptic hydrophobic interaction between CENP-T and Spc25 resulting in a phospho-regulated interaction that occurs without direct recognition of the phosphorylated residue. The Ndc80 complex interacts with both CENP-T and the Mis12 complex, but we find that these interactions are mutually exclusive, supporting a model in which two distinct pathways target the Ndc80 complex to kinetochores. Our results provide a model for how the multiple protein complexes at kinetochores associate in a phospho-regulated manner.
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173
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Đordić A, Egelseer EM, Tesarz M, Sleytr UB, Keller W, Pavkov-Keller T. Crystallization of domains involved in self-assembly of the S-layer protein SbsC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1511-4. [PMID: 23192035 PMCID: PMC3509976 DOI: 10.1107/s1744309112042650] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/11/2012] [Indexed: 12/02/2022]
Abstract
The Gram-positive bacterium Geobacillus stearothermophilus ATCC 12980 is completely covered with a two-dimensional crystalline monolayer composed of the S-layer protein SbsC. In order to complete the structure of the full-length protein, additional soluble constructs containing the crucial domains for self-assembly have been successfully cloned, expressed and purified. Crystals obtained from three different recombinant constructs yielded diffraction to 3.4, 2.8 and 1.5 Å resolution. Native data have been collected.
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Affiliation(s)
- Anđela Đordić
- Institute of Molecular Biosciences, Karl-Franzens University Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Eva M. Egelseer
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Manfred Tesarz
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Uwe B. Sleytr
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, Karl-Franzens University Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, Karl-Franzens University Graz, Humboldtstrasse 50, 8010 Graz, Austria
- ACIB (Austrian Centre of Industrial Biotechnology) GmbH, Petersgasse 14, 8010 Graz, Austria
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174
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Lobley CMC, Aller P, Douangamath A, Reddivari Y, Bumann M, Bird LE, Nettleship JE, Brandao-Neto J, Owens RJ, O’Toole PW, Walsh MA. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1427-33. [PMID: 23192019 PMCID: PMC3509960 DOI: 10.1107/s174430911204273x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/12/2012] [Indexed: 11/10/2022]
Abstract
The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.
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Affiliation(s)
- Carina M. C. Lobley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Alice Douangamath
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Yamini Reddivari
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxfordshire OX11 0FA, England
| | - Mario Bumann
- MRC France, BM14, c/o ESRF, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble France
| | - Louise E. Bird
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxfordshire OX11 0FA, England
| | - Joanne E. Nettleship
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxfordshire OX11 0FA, England
| | - Jose Brandao-Neto
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Raymond J. Owens
- Oxford Protein Production Facility UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxfordshire OX11 0FA, England
| | - Paul W. O’Toole
- Department of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
- MRC France, BM14, c/o ESRF, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble France
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175
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Chauviac FX, Bommer M, Yan J, Parkin G, Daviter T, Lowden P, Raven EL, Thalassinos K, Keep NH. Crystal structure of reduced MsAcg, a putative nitroreductase from Mycobacterium smegmatis and a close homologue of Mycobacterium tuberculosis Acg. J Biol Chem 2012; 287:44372-83. [PMID: 23148223 DOI: 10.1074/jbc.m112.406264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This paper presents the structure of MsAcg (MSMEG_5246), a Mycobacterium smegmatis homologue of Mycobacterium tuberculosis Acg (Rv2032) in its reduced form at 1.6 Å resolution using x-ray crystallography. Rv2032 is one of the most induced genes under the hypoxic model of tuberculosis dormancy. The Acg family turns out to be unusual flavin mononucleotide (FMN)-binding proteins that have probably arisen by gene duplication and fusion from a classical homodimeric nitroreductase such that the monomeric protein resembles a classical nitroreductase dimer but with one active site deleted and the other active site covered by a unique lid. The FMN cofactor is not reduced by either NADH or NADPH, but the chemically reduced enzyme is capable of reduction of nitro substrates, albeit at no kinetic advantage over free FMN. The reduced enzyme is rapidly oxidized by oxygen but without any evidence for a radical state commonly seen in oxygen-sensitive nitroreductases. The presence of the unique lid domain, the lack of reduction by NAD(P)H, and the slow rate of reaction of the chemically reduced protein raises a possible alternative function of Acg proteins in FMN storage or sequestration from other biochemical pathways as part of the bacteria's adaptation to a dormancy state.
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Affiliation(s)
- François-Xavier Chauviac
- Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, United Kingdom
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176
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Grinter R, Roszak AW, Cogdell RJ, Milner JJ, Walker D. The crystal structure of the lipid II-degrading bacteriocin syringacin M suggests unexpected evolutionary relationships between colicin M-like bacteriocins. J Biol Chem 2012; 287:38876-88. [PMID: 22995910 DOI: 10.1074/jbc.m112.400150] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Colicin-like bacteriocins show potential as next generation antibiotics with clinical and agricultural applications. Key to these potential applications is their high potency and species specificity that enables a single pathogenic species to be targeted with minimal disturbance of the wider microbial community. Here we present the structure and function of the colicin M-like bacteriocin, syringacin M from Pseudomonas syringae pv. tomato DC3000. Syringacin M kills susceptible cells through a highly specific phosphatase activity that targets lipid II, ultimately inhibiting peptidoglycan synthesis. Comparison of the structures of syringacin M and colicin M reveals that, in addition to the expected similarity between the homologous C-terminal catalytic domains, the receptor binding domains of these proteins, which share no discernible sequence homology, share a striking structural similarity. This indicates that the generation of the novel receptor binding and species specificities of these bacteriocins has been driven by diversifying selection rather than diversifying recombination as suggested previously. Additionally, the structure of syringacin M reveals the presence of an active site calcium ion that is coordinated by a conserved aspartic acid side chain and is essential for catalytic activity. We show that mutation of this residue to alanine inactivates syringacin M and that the metal ion is absent from the structure of the mutant protein. Consistent with the presence of Ca(2+) in the active site, we show that syringacin M activity is supported by Ca(2+), along with Mg(2+) and Mn(2+), and the protein is catalytically inactive in the absence of these ions.
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Affiliation(s)
- Rhys Grinter
- Institute of Infection, Immunity, and Inflammation, School of Life Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, Scotland, United Kingdom
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177
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Evnouchidou I, Birtley J, Seregin S, Papakyriakou A, Zervoudi E, Samiotaki M, Panayotou G, Giastas P, Petrakis O, Georgiadis D, Amalfitano A, Saridakis E, Mavridis IM, Stratikos E. A common single nucleotide polymorphism in endoplasmic reticulum aminopeptidase 2 induces a specificity switch that leads to altered antigen processing. THE JOURNAL OF IMMUNOLOGY 2012; 189:2383-92. [PMID: 22837489 DOI: 10.4049/jimmunol.1200918] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) cooperate to trim antigenic peptide precursors for loading onto MHC class I molecules and help regulate the adaptive immune response. Common coding single nucleotide polymorphisms in ERAP1 and ERAP2 have been linked with predisposition to human diseases ranging from viral and bacterial infections to autoimmunity and cancer. It has been hypothesized that altered Ag processing by these enzymes is a causal link to disease etiology, but the molecular mechanisms are obscure. We report in this article that the common ERAP2 single nucleotide polymorphism rs2549782 that codes for amino acid variation N392K leads to alterations in both the activity and the specificity of the enzyme. Specifically, the 392N allele excises hydrophobic N-terminal residues from epitope precursors up to 165-fold faster compared with the 392K allele, although both alleles are very similar in excising positively charged N-terminal amino acids. These effects are primarily due to changes in the catalytic turnover rate (k(cat)) and not in the affinity for the substrate. X-ray crystallographic analysis of the ERAP2 392K allele suggests that the polymorphism interferes with the stabilization of the N terminus of the peptide both directly and indirectly through interactions with key residues participating in catalysis. This specificity switch allows the 392N allele of ERAP2 to supplement ERAP1 activity for the removal of hydrophobic N-terminal residues. Our results provide mechanistic insight to the association of this ERAP2 polymorphism with disease and support the idea that polymorphic variation in Ag processing enzymes constitutes a component of immune response variability in humans.
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Affiliation(s)
- Irini Evnouchidou
- National Center for Scientific Research Demokritos, 15310 Athens, Greece
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178
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Schuller JM, Zocher G, Liebhold M, Xie X, Stahl M, Li SM, Stehle T. Structure and catalytic mechanism of a cyclic dipeptide prenyltransferase with broad substrate promiscuity. J Mol Biol 2012; 422:87-99. [PMID: 22683356 DOI: 10.1016/j.jmb.2012.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/11/2012] [Accepted: 05/13/2012] [Indexed: 11/30/2022]
Abstract
Fungal indole prenyltransferases (PTs) typically act on specific substrates, and they are able to prenylate their target compounds with remarkably high regio- and stereoselectivity. Similar to several indole PTs characterized to date, the cyclic dipeptide N-prenyltransferase (CdpNPT) is able to prenylate a range of diverse substrates, thus exhibiting an unusually broad substrate promiscuity. To define the structural basis for this promiscuity, we have determined crystal structures of unliganded CdpNPT and of a ternary complex of CdpNPT bound to (S)-benzodiazepinedione and thiolodiphosphate. Analysis of the structures reveals a limited number of specific interactions with (S)-benzodiazepinedione, which projects into a largely hydrophobic surface. This surface can also accommodate other substrates, explaining the ability of the enzyme to prenylate a range of compounds. The location of the bound substrates suggests a likely reaction mechanism for the conversion of (S)-benzodiazepinedione. Structure-guided mutagenesis experiments confirm that, in addition to (S)-benzodiazepinedione, CdpNPT can also act on (R)-benzodiazepinedione and several cyclic dipeptides, albeit with relaxed specificity. Finally, nuclear magnetic resonance spectroscopy demonstrates that CdpNPT is a C-3 reverse PT that catalyzes the formation of C-3β prenylated indolines from diketopiperazines of tryptophan-containing cyclic dipeptides.
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Affiliation(s)
- Jan Michael Schuller
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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179
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Lyskowski A, Tengg M, Steinkellner G, Schwab H, Gruber-Khadjawi M, Gruber K. Crystallization of the novel S-adenosyl-L-methionine-dependent C-methyltransferase CouO from Streptomyces rishiriensis and preliminary diffraction data analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:698-700. [PMID: 22684074 PMCID: PMC3370914 DOI: 10.1107/s1744309112017137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/18/2012] [Indexed: 11/10/2022]
Abstract
Recombinant Q9F8T9 protein from Streptomyces rishiriensis (CouO), an S-adenosyl-L-methionine-dependent C-methyltransferase, has been successfully cloned, expressed and purified. CouO was crystallized from a single condition in the Morpheus crystallization screen. A vitrified crystal diffracted to 2.05 Å resolution and belonged to space group P2(1), with unit-cell parameters a = 33.02, b = 82.87, c = 76.77 Å, β = 96.93°.
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Affiliation(s)
- Andrzej Lyskowski
- AAustrian Centre of Industrial Biotechnology, GmbH, Petersgasse 14, 8010 Graz, Austria.
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180
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Łyskowski A, Steiner K, Hajnal I, Steinkellner G, Schwab H, Gruber K. Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:451-4. [PMID: 22505418 PMCID: PMC3325818 DOI: 10.1107/s1744309112006550] [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: 12/20/2011] [Accepted: 02/14/2012] [Indexed: 01/29/2023]
Abstract
Recombinant AciX9_0562 from Acidobacterium sp. MP5ACTX9 (UniProt ID E8WYN5) containing sequence motifs characteristic of the RmlC-type cupins superfamily and containing Pfam motif PF07883 has been successfully cloned, expressed and purified. AciX9_0562 crystallized in a number of conditions from the Morpheus protein crystallization screen. The best crystal diffracted to 2.7 Å resolution (space group C222(1); unit-cell parameters a = 125.29, b = 254.63, c = 82.99 Å). Structure solution was facilitated by the automated molecular-replacement pipeline BALBES. The initial solution was automatically rebuilt using the PHENIX AutoBuild wizard, with final R and R(free) values of 0.23 and 0.26, respectively. The structure is currently undergoing manual refinement.
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Affiliation(s)
- Andrzej Łyskowski
- ACIB - Austrian Centre of Industrial Biotechnology GmbH, Petersgasse 14, 8010 Graz, Austria.
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181
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Huculeci R, Buts L, Lenaerts T, van Nuland NAJ, Garcia-Pino A. Purification, crystallization and preliminary X-ray diffraction analysis of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:359-64. [PMID: 22442244 PMCID: PMC3310552 DOI: 10.1107/s1744309112004186] [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: 12/14/2011] [Accepted: 01/31/2012] [Indexed: 11/10/2022]
Abstract
SH2 domains are widespread protein-binding modules that recognize phosphotyrosines and play central roles in intracellular signalling pathways. The SH2 domain of the human protein tyrosine kinase Fyn has been expressed, purified and crystallized in the unbound state and in complex with a high-affinity phosphotyrosine peptide. X-ray data were collected to a resolution of 2.00 Å for the unbound form and 1.40 Å for the protein in complex with the phosphotyrosine peptide.
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Affiliation(s)
- Radu Huculeci
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Lieven Buts
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Tom Lenaerts
- MLG, Département d’Informatique, Université Libre de Bruxelles, Boulevard du Triomphe CP212, B-1050 Brussels, Belgium
- AI-lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Nico A. J. van Nuland
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
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182
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Griffiths S, Byrne RT, Antson AA, Whelan F. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:333-6. [PMID: 22442237 DOI: 10.1107/s1744309112003831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/29/2012] [Indexed: 11/11/2022]
Abstract
Dihydrouridine synthases catalyse the reduction of uridine to dihydrouridine in the D-loop and variable loop of tRNA. The human dihydrouridine synthase HsDus2L has been implicated in the development of pulmonary carcinogenesis. Here, the purification, crystallization and preliminary X-ray characterization of the HsDus2L catalytic domain are reported. The crystals belonged to space group P2(1) and contained a single molecule of HsDus2L in the asymmetric unit. A complete data set was collected to 1.9 Å resolution using synchrotron radiation.
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Affiliation(s)
- Sam Griffiths
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, England
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183
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Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F. On the need for an international effort to capture, share and use crystallization screening data. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:253-8. [PMID: 22442216 PMCID: PMC3310524 DOI: 10.1107/s1744309112002618] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/20/2012] [Indexed: 11/10/2022]
Abstract
Development of an ontology for the description of crystallization experiments and results is proposed. When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange (XDX) workshop organized by several international large-scale crystallization screening laboratories to discuss how this information may be captured and utilized. A group that administers a significant fraction of the world’s crystallization screening results was convened, together with chemical and structural data informaticians and computational scientists who specialize in creating and analysing large disparate data sets. The development of a crystallization ontology for the crystallization community was proposed. This paper (by the attendees of the workshop) provides the thoughts and rationale leading to this conclusion. This is brought to the attention of the wider audience of crystallographers so that they are aware of these early efforts and can contribute to the process going forward.
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Affiliation(s)
- Janet Newman
- Materials Science and Engineering, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.
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184
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Saleem M, Prince SM, Patel H, Chan H, Feavers IM, Derrick JP. Refolding, purification and crystallization of the FrpB outer membrane iron transporter from Neisseria meningitidis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:231-5. [PMID: 22298007 PMCID: PMC3274411 DOI: 10.1107/s1744309111056028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 12/28/2011] [Indexed: 11/10/2022]
Abstract
FrpB is an integral outer membrane protein from the human pathogen Neisseria meningitidis. It is a member of the TonB-dependent transporter family and promotes the uptake of iron across the outer membrane. There is also evidence that FrpB is an antigen and hence a potential component of a vaccine against meningococcal meningitis. FrpB incorporating a polyhistidine tag was overexpressed in Escherichia coli into inclusion bodies. The protein was then solubilized in urea, refolded and purified to homogeneity. Two separate antigenic variants of FrpB were crystallized by sitting-drop vapour diffusion. Crystals of the F5-1 variant diffracted to 2.4 Å resolution and belonged to space group C2, with unit-cell parameters a = 176.5, b = 79.4, c = 75.9 Å, β = 98.3°. Crystal-packing calculations suggested the presence of a monomer in the asymmetric unit. Crystals of the F3-3 variant also diffracted to 2.4 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 85.3, b = 104.6, c = 269.1 Å. Preliminary analysis suggested the presence of an FrpB trimer in the asymmetric unit.
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Affiliation(s)
- Muhammad Saleem
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, England
| | - Stephen M. Prince
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester, England
| | - Hema Patel
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, England
| | - Hannah Chan
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, England
| | - Ian M. Feavers
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, England
| | - Jeremy P. Derrick
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, England
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185
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Björkelid C, Bergfors T, Unge T, Mowbray SL, Jones TA. Structural studies on Mycobacterium tuberculosis DXR in complex with the antibiotic FR-900098. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:134-43. [PMID: 22281742 DOI: 10.1107/s0907444911052231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/03/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize the essential isoprenoid precursor isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway that is found in humans. As part of a structure-based drug-discovery program against tuberculosis, DXR, the enzyme that carries out the second step in the MEP pathway, has been investigated. This enzyme is the target for the antibiotic fosmidomycin and its active acetyl derivative FR-900098. The structure of DXR from Mycobacterium tuberculosis in complex with FR-900098, manganese and the NADPH cofactor has been solved and refined. This is a new crystal form that diffracts to a higher resolution than any other DXR complex reported to date. Comparisons with other ternary complexes show that the conformation is that of the enzyme in an active state: the active-site flap is well defined and the cofactor-binding domain has a conformation that brings the NADPH into the active site in a manner suitable for catalysis. The substrate-binding site is highly conserved in a number of pathogens that use this pathway, so any new inhibitor that is designed for the M. tuberculosis enzyme is likely to exhibit broad-spectrum activity.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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186
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Saleem M, Moore J, Derrick JP. Expression, purification, and crystallization of neisserial outer membrane proteins. Methods Mol Biol 2012; 799:91-106. [PMID: 21993641 DOI: 10.1007/978-1-61779-346-2_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Integral outer membrane proteins (OMPs) play key roles in solute transport, adhesion, and other processes. In Neisseria, they can also function as major protective antigens. Structural, biophysical, and immunological studies of Neisserial OMPs require their isolation in milligram quantities. Purification of any OMP directly from Neisseria would require the growth of large quantities of cell mass, with attendant concerns about safety and convenience. As a result, many investigators have developed methods for expression of OMPs into inclusion bodies in E. coli, followed by refolding of the resolubilized protein. Here we describe such a method, as optimized for the PorA porin but which can be applied, with suitable adaptation, to other OMPs. We also describe an approach to the crystallization of PorA.
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187
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Birtley JR, Saridakis E, Stratikos E, Mavridis IM. The Crystal Structure of Human Endoplasmic Reticulum Aminopeptidase 2 Reveals the Atomic Basis for Distinct Roles in Antigen Processing. Biochemistry 2011; 51:286-95. [DOI: 10.1021/bi201230p] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- James R. Birtley
- Structural and Supramolecular Chemistry Laboratory, Institute of
Physical Chemistry, National Center for Scientific Research Demokritos, Aghia Paraskevi 15310, Athens, Greece
| | - Emmanuel Saridakis
- Structural and Supramolecular Chemistry Laboratory, Institute of
Physical Chemistry, National Center for Scientific Research Demokritos, Aghia Paraskevi 15310, Athens, Greece
| | - Efstratios Stratikos
- Protein Chemistry Laboratory,
IRRP, National Center for Scientific Research Demokritos, Aghia Paraskevi 15310, Athens, Greece
| | - Irene M. Mavridis
- Structural and Supramolecular Chemistry Laboratory, Institute of
Physical Chemistry, National Center for Scientific Research Demokritos, Aghia Paraskevi 15310, Athens, Greece
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188
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Lee BG, Kim MK, Song HK. Structural insights into the conformational diversity of ClpP from Bacillus subtilis. Mol Cells 2011; 32:589-95. [PMID: 22080375 PMCID: PMC3887684 DOI: 10.1007/s10059-011-0197-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 10/15/2022] Open
Abstract
ClpP is a cylindrical protease that is tightly regulated by Clp-ATPases. The activation mechanism of ClpP using acyldepsipeptide antibiotics as mimics of natural activators showed enlargement of the axial entrance pore for easier processing of incoming substrates. However, the elimination of degradation products from inside the ClpP chamber remains unclear since there is no exit pore for releasing these products in all determined ClpP structures. Here we report a new crystal structure of ClpP from Bacillus subtilis, which shows a significantly compressed shape along the axial direction. A portion of the handle regions comprising the heptameric ring-ring contacts shows structural transition from an ordered to a disordered state, which triggers the large conformational change from an extended to an overall compressed structure. Along with this structural change, 14 side pores are generated for product release and the catalytic triad adopts an inactive orientation. We have also determined B. subtilis ClpP inhibited by diisopropylfluoro-phosphate and analyzed the active site in detail. Structural information pertaining to several different conformational steps such as those related to extended, ADEP-activated, DFP-inhibited and compressed forms of ClpP from B. subtilis is available. Structural comparisons suggest that functionally important regions in the ClpP-family such as N-terminal segments for the axial pore, catalytic triads, and handle domains for the product releasing pore exhibit intrinsically dynamic and unique structural features. This study provides valuable insights for understanding the enigmatic cylindrical degradation machinery of ClpP as well as other related proteases such as HslV and the 20S proteasome.
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Affiliation(s)
| | | | - Hyun Kyu Song
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
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189
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Gonçalves S, Esteves AM, Santos H, Borges N, Matias PM. Three-Dimensional Structure of Mannosyl-3-phosphoglycerate Phosphatase from Thermus thermophilus HB27: A New Member of the Haloalcanoic Acid Dehalogenase Superfamily. Biochemistry 2011; 50:9551-67. [DOI: 10.1021/bi201171h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susana Gonçalves
- ITQB-Instituto
de Tecnologia Quı́mica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Ana M. Esteves
- ITQB-Instituto
de Tecnologia Quı́mica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Helena Santos
- ITQB-Instituto
de Tecnologia Quı́mica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Nuno Borges
- ITQB-Instituto
de Tecnologia Quı́mica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Pedro M. Matias
- ITQB-Instituto
de Tecnologia Quı́mica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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190
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Kim SE, Bahta M, Lountos GT, Ulrich RG, Burke TR, Waugh DS. Isothiazolidinone (IZD) as a phosphoryl mimetic in inhibitors of the Yersinia pestis protein tyrosine phosphatase YopH. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:639-45. [PMID: 21697602 PMCID: PMC3121299 DOI: 10.1107/s0907444911018610] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 05/16/2011] [Indexed: 11/10/2022]
Abstract
Isothiazolidinone (IZD) heterocycles can act as effective components of protein tyrosine phosphatase (PTP) inhibitors by simultaneously replicating the binding interactions of both a phosphoryl group and a highly conserved water molecule, as exemplified by the structures of several PTP1B-inhibitor complexes. In the first unambiguous demonstration of IZD interactions with a PTP other than PTP1B, it is shown by X-ray crystallography that the IZD motif binds within the catalytic site of the Yersinia pestis PTP YopH by similarly displacing a highly conserved water molecule. It is also shown that IZD-based bidentate ligands can inhibit YopH in a nonpromiscuous fashion at low micromolar concentrations. Hence, the IZD moiety may represent a useful starting point for the development of YopH inhibitors.
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Affiliation(s)
- Sung-Eun Kim
- Chemical Biology Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
| | - Medhanit Bahta
- Chemical Biology Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
| | - George T. Lountos
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
| | - Robert G. Ulrich
- Laboratory of Molecular Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
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191
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Bahta M, Lountos GT, Dyas B, Kim SE, Ulrich RG, Waugh DS, Burke TR. Utilization of nitrophenylphosphates and oxime-based ligation for the development of nanomolar affinity inhibitors of the Yersinia pestis outer protein H (YopH) phosphatase. J Med Chem 2011; 54:2933-43. [PMID: 21443195 PMCID: PMC3085962 DOI: 10.1021/jm200022g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Our current study reports the first K(M) optimization of a library of nitrophenylphosphate-containing substrates for generating an inhibitor lead against the Yersinia pestis outer protein phosphatase (YopH). A high activity substrate identified by this method (K(M) = 80 μM) was converted from a substrate into an inhibitor by replacement of its phosphate group with difluoromethylphosphonic acid and by attachment of an aminooxy handle for further structural optimization by oxime ligation. A cocrystal structure of this aminooxy-containing platform in complex with YopH allowed the identification of a conserved water molecule proximal to the aminooxy group that was subsequently employed for the design of furanyl-based oxime derivatives. By this process, a potent (IC(50) = 190 nM) and nonpromiscuous inhibitor was developed with good YopH selectivity relative to a panel of phosphatases. The inhibitor showed significant inhibition of intracellular Y. pestis replication at a noncytotoxic concentration. The current work presents general approaches to PTP inhibitor development that may be useful beyond YopH.
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Affiliation(s)
- Medhanit Bahta
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, U.S.A
| | - George T. Lountos
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Beverly Dyas
- Laboratory of Molecular Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, U.S.A
| | - Sung-Eun Kim
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Robert G. Ulrich
- Laboratory of Molecular Immunology, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland 21702, U.S.A
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, U.S.A
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192
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Björkelid C, Bergfors T, Henriksson LM, Stern AL, Unge T, Mowbray SL, Jones TA. Structural and functional studies of mycobacterial IspD enzymes. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:403-14. [PMID: 21543842 DOI: 10.1107/s0907444911006160] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/18/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway found in humans. As part of a structure-based drug-discovery program against tuberculosis, IspD, the enzyme that carries out the third step in the MEP pathway, was targeted. Constructs of both the Mycobacterium smegmatis and the Mycobacterium tuberculosis enzymes that were suitable for structural and inhibitor-screening studies were engineered. Two crystal structures of the M. smegmatis enzyme were produced, one in complex with CTP and the other in complex with CMP. In addition, the M. tuberculosis enzyme was crystallized in complex with CTP. Here, the structure determination and crystallographic refinement of these crystal forms and the enzymatic characterization of the M. tuberculosis enzyme construct are reported. A comparison with known IspD structures allowed the definition of the structurally conserved core of the enzyme. It indicates potential flexibility in the enzyme and in particular in areas close to the active site. These well behaved constructs provide tools for future target-based screening of potential inhibitors. The conserved nature of the extended active site suggests that any new inhibitor will potentially exhibit broad-spectrum activity.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-75124 Uppsala, Sweden
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193
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Gonçalves S, Esteves AM, Borges N, Santos H, Matias PM. Crystallization and preliminary X-ray analysis of mannosyl-3-phosphoglycerate phosphatase from Thermus thermophilus HB27. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:390-6. [PMID: 21393850 PMCID: PMC3053170 DOI: 10.1107/s1744309111002843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/20/2011] [Indexed: 11/11/2022]
Abstract
Mannosylglycerate (MG) is primarily known as an osmolyte and is widely distributed among (hyper)thermophilic marine microorganisms. The synthesis of MG via mannosyl-3-phosphoglycerate synthase (MpgS) and mannosyl-3-phosphoglycerate phosphatase (MpgP), the so-called two-step pathway, is the most prevalent route among these organisms. The phosphorylated intermediate mannosyl-3-phosphoglycerate is synthesized by the first enzyme and is subsequently dephosphorylated by the second. The structure of MpgS from the thermophilic bacterium Thermus thermophilus HB27 has recently been solved and characterized. Here, the cloning, expression, purification, crystallization and preliminary crystallographic analysis of MpgP from T. thermophilus HB27 are reported. Size-exclusion chromatography assays suggested a dimeric assembly in solution for MpgP at pH 6.3 and together with differential scanning fluorimetry data showed that high ionic strength and charge compensation were required to produce a highly pure and soluble protein sample for crystallographic studies. The crystals obtained belonged to the monoclinic space group P2(1), with unit-cell parameters a=39.52, b=70.68, c=95.42 Å, β=92.95°. Diffraction data were measured to 1.9 Å resolution. Matthews coefficient calculations suggested the presence of two MpgP monomers in the asymmetric unit and the calculation of a self-rotation Patterson map indicated that the two monomers could be related by a noncrystallographic twofold rotation axis, forming a dimer.
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Affiliation(s)
- Susana Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Ana M. Esteves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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