101
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Ting YT, Petersen J, Ramarathinam SH, Scally SW, Loh KL, Thomas R, Suri A, Baker DG, Purcell AW, Reid HH, Rossjohn J. The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis. J Biol Chem 2018; 293:3236-3251. [PMID: 29317506 DOI: 10.1074/jbc.ra117.001013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/21/2017] [Indexed: 12/22/2022] Open
Abstract
The HLA-DRB1 locus is strongly associated with rheumatoid arthritis (RA) susceptibility, whereupon citrullinated self-peptides bind to HLA-DR molecules bearing the shared epitope (SE) amino acid motif. However, the differing propensity for citrullinated/non-citrullinated self-peptides to bind given HLA-DR allomorphs remains unclear. Here, we used a fluorescence polarization assay to determine a hierarchy of binding affinities of 34 self-peptides implicated in RA against three HLA-DRB1 allomorphs (HLA-DRB1*04:01/*04:04/*04:05) each possessing the SE motif. For all three HLA-DRB1 allomorphs, we observed a strong correlation between binding affinity and citrullination at P4 of the bound peptide ligand. A differing hierarchy of peptide-binding affinities across the three HLA-DRB1 allomorphs was attributable to the β-chain polymorphisms that resided outside the SE motif and were consistent with sequences of naturally presented peptide ligands. Structural determination of eight HLA-DR4-self-epitope complexes revealed strict conformational convergence of the P4-Cit and surrounding HLA β-chain residues. Polymorphic residues that form part of the P1 and P9 pockets of the HLA-DR molecules provided a structural basis for the preferential binding of the citrullinated self-peptides to the HLA-DR4 allomorphs. Collectively, we provide a molecular basis for the interplay between citrullination of self-antigens and HLA polymorphisms that shape peptide-HLA-DR4 binding affinities in RA.
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Affiliation(s)
- Yi Tian Ting
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Jan Petersen
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Sri H Ramarathinam
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Stephen W Scally
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Khai L Loh
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Ranjeny Thomas
- the University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Anish Suri
- the Janssen Research and Development, Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, B-2340-Beerse, Belgium
| | - Daniel G Baker
- the Janssen Research and Development, LLC, Spring House, Pennsylvania 19002, and
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and
| | - Hugh H Reid
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, and .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
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102
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Zhou RB, Lu XL, Dong C, Ahmad F, Zhang CY, Yin DC. Application of protein crystallization methodologies to enhance the solubility, stability and monodispersity of proteins. CrystEngComm 2018. [DOI: 10.1039/c7ce02189e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Application of protein crystallization methodologies to screen optimal solution formulations for proteins prone to aggregation.
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Affiliation(s)
- Ren-Bin Zhou
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Xiao-Li Lu
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Chen Dong
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Fiaz Ahmad
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Chen-Yan Zhang
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience & Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- PR China
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103
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Arnling Bååth J, Mazurkewich S, Knudsen RM, Poulsen JCN, Olsson L, Lo Leggio L, Larsbrink J. Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:213. [PMID: 30083226 PMCID: PMC6069808 DOI: 10.1186/s13068-018-1213-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/23/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration. RESULTS Ten CE15 enzymes from three bacterial species, sharing as little as 20% sequence identity, were characterized on a range of model substrates; two protein structures were solved, and insights into their regulation and biological roles were gained through gene expression analysis and enzymatic assays on complex biomass. Several enzymes with higher catalytic efficiencies on a wider range of model substrates than previously characterized fungal GEs were identified. Similarities and differences regarding substrate specificity between the investigated GEs were observed and putatively linked to their positioning in the CE15 phylogenetic tree. The bacterial GEs were able to utilize substrates lacking 4-OH methyl substitutions, known to be important for fungal enzymes. In addition, certain bacterial GEs were able to efficiently cleave esters of galacturonate, a functionality not previously described within the family. The two solved structures revealed similar overall folds to known structures, but also indicated active site regions allowing for more promiscuous substrate specificities. The gene expression analysis demonstrated that bacterial GE-encoding genes were differentially expressed as response to different carbon sources. Further, improved enzymatic saccharification of milled corn cob by a commercial lignocellulolytic enzyme cocktail when supplemented with GEs showcased their synergistic potential with other enzyme types on native biomass. CONCLUSIONS Bacterial GEs exhibit much larger diversity than fungal counterparts. In this study, we significantly expanded the existing knowledge on CE15 with the in-depth characterization of ten bacterial GEs broadly spanning the phylogenetic tree, and also presented two novel enzyme structures. Variations in transcriptional responses of CE15-encoding genes under different growth conditions suggest nonredundant functions for enzymes found in species with multiple CE15 genes and further illuminate the importance of GEs in native lignin-carbohydrate disassembly.
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Affiliation(s)
- Jenny Arnling Bååth
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Lisbeth Olsson
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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104
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Pinotsis N, Waksman G. Crystal structure of the Legionella pneumophila Lpg2936 in complex with the cofactor S-adenosyl-L-methionine reveals novel insights into the mechanism of RsmE family methyltransferases. Protein Sci 2017; 26:2381-2391. [PMID: 28940762 PMCID: PMC5699498 DOI: 10.1002/pro.3305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022]
Abstract
The methylation of U1498 located in the 16S ribosomal RNA of Escherichia coli is an important modification affecting ribosomal activity. RsmE methyltransferases methylate specifically this position in a mechanism that requires an S‐adenosyl‐L‐methionine (AdoMet) molecule as cofactor. Here we report the structure of Apo and AdoMet‐bound Lpg2936 from Legionella pneumophila at 1.5 and 2.3 Å, respectively. The protein comprises an N‐terminal PUA domain and a C‐terminal SPOUT domain. The latter is responsible for protein dimerization and cofactor binding. Comparison with similar structures suggests that Lpg2936 is an RsmE‐like enzyme that can target the equivalent of U1498 in the L. pneumophila ribosomal RNA, thereby potentially enhancing ribosomal activity during infection‐mediated effector production. The multiple copies of the enzyme found in both structures reveal a flexible conformation of the bound AdoMet ligand. Isothermal titration calorimetry measurements suggest an asymmetric two site binding mode. Our results therefore also provide unprecedented insights into AdoMet/RsmE interaction, furthering our understanding of the RsmE catalytic mechanism. PDB Code(s): 5O95; 5O96
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Affiliation(s)
- Nikos Pinotsis
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, London, United Kingdom
| | - Gabriel Waksman
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, London, United Kingdom.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
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105
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Guo J, Coker AR, Wood SP, Cooper JB, Chohan SM, Rashid N, Akhtar M. Structure and function of the thermostableL-asparaginase fromThermococcus kodakarensis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:889-895. [DOI: 10.1107/s2059798317014711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022]
Abstract
L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase fromThermococcus kodakarensis(TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85°C. It has aKmvalue of 5.5 mMfor L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 Å resolution, confirming the presence of two α/β domains connected by a short linker region. The N-terminal domain contains a highly flexible β-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this β-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes.
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106
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Nakatani Y, Jiao W, Aragão D, Shimaki Y, Petri J, Parker EJ, Cook GM. Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å. Acta Crystallogr F Struct Biol Commun 2017; 73:541-549. [PMID: 28994401 PMCID: PMC5633920 DOI: 10.1107/s2053230x17013073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022] Open
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - David Aragão
- Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Australia
| | - Yosuke Shimaki
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Jessica Petri
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
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107
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Calvopiña K, Hinchliffe P, Brem J, Heesom KJ, Johnson S, Cain R, Lohans CT, Fishwick CWG, Schofield CJ, Spencer J, Avison MB. Structural/mechanistic insights into the efficacy of nonclassical β-lactamase inhibitors against extensively drug resistantStenotrophomonas maltophiliaclinical isolates. Mol Microbiol 2017; 106:492-504. [DOI: 10.1111/mmi.13831] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Karina Calvopiña
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Philip Hinchliffe
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Jürgen Brem
- Department of Chemistry; University of Oxford; Oxford UK
| | | | - Samar Johnson
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Ricky Cain
- School of Chemistry; University of Leeds; Leeds UK
| | | | | | | | - James Spencer
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Matthew B. Avison
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
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108
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Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD + Binding and the Cofactor Positioned to Accept a Hydride. Sci Rep 2017; 7:10476. [PMID: 28874718 PMCID: PMC5585171 DOI: 10.1038/s41598-017-10859-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/11/2017] [Indexed: 12/28/2022] Open
Abstract
Plants, lower eukaryotes, bacteria, and archaebacteria synthesise L-histidine (His) in a similar, multistep pathway that is absent in mammals. This makes the His biosynthetic route a promising target for herbicides, antifungal agents, and antibiotics. The last enzyme of the pathway, bifunctional L-histidinol dehydrogenase (HDH, EC 1.1.1.23), catalyses two oxidation reactions: from L-histidinol (HOL) to L-histidinaldehyde and from L-histidinaldehyde to His. Over the course of the reaction, HDH utilises two molecules of NAD+ as the hydride acceptor. The object of this study was the HDH enzyme from the model legume plant, Medicago truncatula (MtHDH). Three crystal structures complexed with imidazole, HOL, and His with NAD+ provided in-depth insights into the enzyme architecture, its active site, and the cofactor binding mode. The overall structure of MtHDH is similar to the two bacterial orthologues whose three-dimensional structures have been determined. The three snapshots, with the MtHDH enzyme captured in different states, visualise structural rearrangements that allow for NAD+ binding for the first time. Furthermore, the MtHDH complex with His and NAD+ displays the cofactor molecule situated in a way that would allow for a hydride transfer.
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109
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Capturing LTA 4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB 4 synthesis. Proc Natl Acad Sci U S A 2017; 114:9689-9694. [PMID: 28827365 DOI: 10.1073/pnas.1710850114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human leukotriene (LT) A4 hydrolase/aminopeptidase (LTA4H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA4 into LTB4, a potent leukocyte activating agent, while the aminopeptidase activity cleaves and inactivates the chemotactic tripeptide Pro-Gly-Pro. Here, we describe high-resolution crystal structures of LTA4H complexed with LTA4, providing the structural underpinnings of the enzyme's unique epoxide hydrolase (EH) activity, involving Zn2+, Y383, E271, D375, and two catalytic waters. The structures reveal that a single catalytic water is involved in both catalytic activities of LTA4H, alternating between epoxide ring opening and peptide bond hydrolysis, assisted by E271 and E296, respectively. Moreover, we have found two conformations of LTA4H, uncovering significant domain movements. The resulting structural alterations indicate that LTA4 entrance into the active site is a dynamic process that includes rearrangement of three moving domains to provide fast and efficient alignment and processing of the substrate. Thus, the movement of one dynamic domain widens the active site entrance, while another domain acts like a lid, opening and closing access to the hydrophobic tunnel, which accommodates the aliphatic tale of LTA4 during EH reaction. The enzyme-LTA4 complex structures and dynamic domain movements provide critical insights for development of drugs targeting LTA4H.
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110
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Rea D, Van Elzen R, De Winter H, Van Goethem S, Landuyt B, Luyten W, Schoofs L, Van Der Veken P, Augustyns K, De Meester I, Fülöp V, Lambeir AM. Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling. Eur J Med Chem 2017; 139:482-491. [PMID: 28826083 DOI: 10.1016/j.ejmech.2017.08.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
The Gram-negative anaerobe Porphyromonas gingivalis is associated with chronic periodontitis. Clinical isolates of P. gingivalis strains with high dipeptidyl peptidase 4 (DPP4) expression also had a high capacity for biofilm formation and were more infective. The X-ray crystal structure of P. gingivalis DPP4 was solved at 2.2 Å resolution. Despite a sequence identity of 32%, the overall structure of the dimer was conserved between P. gingivalis DPP4 and mammalian orthologues. The structures of the substrate binding sites were also conserved, except for the region called S2-extensive, which is exploited by specific human DPP4 inhibitors currently used as antidiabetic drugs. Screening of a collection of 450 compounds as inhibitors revealed a structure-activity relationship that mimics in part that of mammalian DPP9. The functional similarity between human and bacterial DPP4 was confirmed using 124 potential peptide substrates.
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Affiliation(s)
- Dean Rea
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Roos Van Elzen
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Sebastiaan Van Goethem
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Bart Landuyt
- Animal Physiology and Neurobiology Section, Department of Biology, KULeuven, Naamsestraat 59, B-3000 Leuven, Belgium.
| | - Walter Luyten
- Animal Physiology and Neurobiology Section, Department of Biology, KULeuven, Naamsestraat 59, B-3000 Leuven, Belgium.
| | - Liliane Schoofs
- Animal Physiology and Neurobiology Section, Department of Biology, KULeuven, Naamsestraat 59, B-3000 Leuven, Belgium.
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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111
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Maldonado-Contreras A, Birtley JR, Boll E, Zhao Y, Mumy KL, Toscano J, Ayehunie S, Reinecker HC, Stern LJ, McCormick BA. Shigella depends on SepA to destabilize the intestinal epithelial integrity via cofilin activation. Gut Microbes 2017; 8:544-560. [PMID: 28598765 PMCID: PMC5730386 DOI: 10.1080/19490976.2017.1339006] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shigella is unique among enteric pathogens, as it invades colonic epithelia through the basolateral pole. Therefore, it has evolved the ability to breach the intestinal epithelial barrier to deploy an arsenal of effector proteins, which permits bacterial invasion and leads to a severe inflammatory response. However, the mechanisms used by Shigella to regulate epithelial barrier permeability remain unknown. To address this question, we used both an intestinal polarized model and a human ex-vivo model to further characterize the early events of host-bacteria interactions. Our results showed that secreted Serine Protease A (SepA), which belongs to the serine protease autotransporter of Enterobacteriaceae family, is responsible for critically disrupting the intestinal epithelial barrier. Such disruption facilitates bacterial transit to the basolateral pole of the epithelium, ultimately fostering the hallmarks of the disease pathology. SepA was found to cause a decrease in active LIM Kinase 1 (LIMK1) levels, a negative inhibitor of actin-remodeling proteins, namely cofilin. Correspondingly, we observed increased activation of cofilin, a major actin-polymerization factor known to control opening of tight junctions at the epithelial barrier. Furthermore, we resolved the crystal structure of SepA to elucidate its role on actin-dynamics and barrier disruption. The serine protease activity of SepA was found to be required for the regulatory effects on LIMK1 and cofilin, resulting in the disruption of the epithelial barrier during infection. Altogether, we demonstrate that SepA is indispensable for barrier disruption, ultimately facilitating Shigella transit to the basolateral pole where it effectively invades the epithelium.
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Affiliation(s)
- Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, University of Massachusetts, Medical School, Worcester, MA, USA,CONTACT Beth A. McCormick ; Ana Maldonado-Contreras 55 Lake Ave N, Worcester, MA, 01655
| | - James R. Birtley
- Department of Pathology, University of Massachusetts, Medical School, Worcester, MA, USA
| | - Erik Boll
- Statens Serum Institut, Copenhagen, Denmark
| | - Yun Zhao
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Karen L. Mumy
- Naval Medical Research Unit Dayton, Wright-Patterson Air Force Base, Dayton, OH, USA
| | - Juan Toscano
- Department of Microbiology and Physiological Systems, University of Massachusetts, Medical School, Worcester, MA, USA
| | | | - Hans-Christian Reinecker
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lawrence J. Stern
- Department of Pathology, University of Massachusetts, Medical School, Worcester, MA, USA
| | - Beth A. McCormick
- Department of Microbiology and Physiological Systems, University of Massachusetts, Medical School, Worcester, MA, USA,CONTACT Beth A. McCormick ; Ana Maldonado-Contreras 55 Lake Ave N, Worcester, MA, 01655
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112
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Bacterial protease uses distinct thermodynamic signatures for substrate recognition. Sci Rep 2017; 7:2848. [PMID: 28588213 PMCID: PMC5460201 DOI: 10.1038/s41598-017-03220-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 12/30/2022] Open
Abstract
Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme (“entropy reservoirs”). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.
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113
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Heggelund JE, Mackenzie A, Martinsen T, Heim JB, Cheshev P, Bernardi A, Krengel U. Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Sci Rep 2017; 7:2326. [PMID: 28539625 PMCID: PMC5443773 DOI: 10.1038/s41598-017-02179-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Cholera is a life-threatening disease in many countries, and new drugs are clearly needed. C-glycosidic antagonists may serve such a purpose. Here we report atomic-resolution crystal structures of three such compounds in complexes with the cholera toxin. The structures give unprecedented atomic details of the molecular interactions and show how the inhibitors efficiently block the GM1 binding site. These molecules are well suited for development into low-cost prophylactic drugs, due to their relatively easy synthesis and their resistance to glycolytic enzymes. One of the compounds links two toxin B-pentamers in the crystal structure, which may yield improved inhibition through the formation of toxin aggregates. These structures can spark the improved design of GM1 mimics, either alone or as multivalent inhibitors connecting multiple GM1-binding sites. Future developments may further include compounds that link the primary and secondary binding sites. Serving as decoys, receptor mimics may lessen symptoms while avoiding the use of antibiotics.
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Affiliation(s)
- Julie Elisabeth Heggelund
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway. .,School of Biomedical Sciences, University of Leeds, LS2 9JT Leeds, UK and School of Pharmacy, University of Oslo, P.O. Box 1068, NO-0316, Blindern, Norway.
| | - Alasdair Mackenzie
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway.,Alere Technologies AS, Kjelsåsveien 161, NO-0884, Oslo, Norway
| | - Tobias Martinsen
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway
| | - Joel Benjamin Heim
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway
| | - Pavel Cheshev
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, 20133, Milano, Italy.,Skolkovo innovation center, Office 229, OC Technopark bld. 2, Lugovaya str. 4, 143026, Moscow, Russia
| | - Anna Bernardi
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, 20133, Milano, Italy
| | - Ute Krengel
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway.
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114
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Mpakali A, Saridakis E, Harlos K, Zhao Y, Kokkala P, Georgiadis D, Giastas P, Papakyriakou A, Stratikos E. Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity. J Med Chem 2017; 60:2963-2972. [PMID: 28328206 DOI: 10.1021/acs.jmedchem.6b01890] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates, although the mechanism behind this wide specificity is not clearly understood. We describe a crystal structure of IRAP in complex with a recently developed bioactive and selective inhibitor at 2.53 Å resolution. In the presence of this inhibitor, the enzyme adopts a novel conformation in which domains II and IV are juxtaposed, forming a hollow structure that excludes external solvent access to the catalytic center. A loop adjacent to the enzyme's GAMEN motif undergoes structural reconfiguration, allowing the accommodation of bulky inhibitor side chains. Atomic interactions between the inhibitor and IRAP that are unique to this conformation can explain the strong selectivity compared to homologous aminopeptidases ERAP1 and ERAP2. This conformation provides insight on IRAP's catalytic cycle and reveals significant active-site plasticity that may underlie its substrate permissiveness.
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Affiliation(s)
- Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | - Emmanuel Saridakis
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University , Oxford OX3 7BN, United Kingdom
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University , Oxford OX3 7BN, United Kingdom
| | - Paraskevi Kokkala
- Department of Chemistry, University of Athens , Athens 15771, Greece
| | | | - Petros Giastas
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
| | | | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece
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115
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Structural and kinetic analysis of Schistosoma mansoni Adenylosuccinate Lyase (SmADSL). Mol Biochem Parasitol 2017; 214:27-35. [PMID: 28347672 DOI: 10.1016/j.molbiopara.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/22/2022]
Abstract
Schistosoma mansoni is the parasite responsible for schistosomiasis, a disease that affects about 218 million people worldwide. Currently, both direct treatment and disease control initiatives rely on chemotherapy using a single drug, praziquantel. Concerns over the possibility of resistance developing to praziquantel, have stimulated efforts to develop new drugs for the treatment of schistosomiasis. Schistosomes do not have the de novo purine biosynthetic pathway, and instead depend entirely on the purine salvage pathway to supply its need for purines. The purine salvage pathway has been reported as a potential target for developing new drugs against schistosomiasis. Adenylosuccinate lyase (SmADSL) is an enzyme in this pathway, which cleaves adenylosuccinate (ADS) into adenosine 5'-monophosphate (AMP) and fumarate. SmADSL kinetic characterization was performed by isothermal titration calorimetry (ITC) using both ADS and SAICAR as substrates. Structures of SmADSL in Apo form and in complex with AMP were elucidated by x-ray crystallography revealing a highly conserved tetrameric structure required for their function since the active sites are formed from residues of three different subunits. The active sites are also highly conserved between species and it is difficult to identify a potent species-specific inhibitor for the development of new therapeutic agents. In contrast, several mutagenesis studies have demonstrated the importance of dimeric interface residues in the stability of the quaternary structure of the enzyme. The lower conservation of these residues between SmADSL and human ADSL could be used to lead the development of anti-schistosomiasis drugs based on disruption of subunit interfaces. These structures and kinetics data add another layer of information to Schistosoma mansoni purine salvage pathway.
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116
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Al-Jassar C, Andreeva A, Barnabas DD, McLaughlin SH, Johnson CM, Yu M, van Breugel M. The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Structure 2016; 25:146-156. [PMID: 28017521 PMCID: PMC5222566 DOI: 10.1016/j.str.2016.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/04/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
Cilia are thin cell projections with essential roles in cell motility, fluid movement, sensing, and signaling. They are templated from centrioles that dock against the plasma membrane and subsequently extend their peripheral microtubule array. The molecular mechanisms underpinning cilia assembly are incompletely understood. Cep104 is a key factor involved in cilia formation and length regulation that rides on the ends of elongating and shrinking cilia. It is mutated in Joubert syndrome, a genetically heterogeneous ciliopathy. Here we provide structural and biochemical data that Cep104 contains a tubulin-binding TOG (tumor overexpressed gene) domain and a novel C2HC zinc finger array. Furthermore, we identify the kinase Nek1, another ciliopathy-associated protein, as a potential binding partner of this array. Finally, we show that Nek1 competes for binding to Cep104 with the distal centriole-capping protein CP110. Our data suggest a model for Cep104 activity during ciliogenesis and provide a novel link between Cep104 and Nek1.
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Affiliation(s)
- Caezar Al-Jassar
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Antonina Andreeva
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Deepak D Barnabas
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen H McLaughlin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Minmin Yu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mark van Breugel
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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117
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Clark KM, Jenkins JL, Fedoriw N, Dumont ME. Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein Sci 2016; 26:242-257. [PMID: 27774687 DOI: 10.1002/pro.3074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022]
Abstract
The function and localization of proteins and peptides containing C-terminal "CaaX" (Cys-aliphatic-aliphatic-anything) sequence motifs are modulated by post-translational attachment of isoprenyl groups to the cysteine sulfhydryl, followed by proteolytic cleavage of the aaX amino acids. The zinc metalloprotease ZMPSTE24 is one of two enzymes known to catalyze this cleavage. The only identified target of mammalian ZMPSTE24 is prelamin A, the precursor to the nuclear scaffold protein lamin A. ZMPSTE24 also cleaves prelamin A at a second site 15 residues upstream from the CaaX site. Mutations in ZMPSTE24 result in premature-aging diseases and inhibition of ZMPSTE24 activity has been reported to be an off-target effect of HIV protease inhibitors. We report here the expression (in yeast), purification, and crystallization of human ZMPSTE24 allowing determination of the structure to 2.0 Å resolution. Compared to previous lower resolution structures, the enhanced resolution provides: (1) a detailed view of the active site of ZMPSTE24, including water coordinating the catalytic zinc; (2) enhanced visualization of fenestrations providing access from the exterior to the interior cavity of the protein; (3) a view of the C-terminus extending away from the main body of the protein; (4) localization of ordered lipid and detergent molecules at internal and external surfaces and also projecting through fenestrations; (5) identification of water molecules associated with the surface of the internal cavity. We also used a fluorogenic assay of the activity of purified ZMPSTE24 to demonstrate that HIV protease inhibitors directly inhibit the human enzyme in a manner indicative of a competitive mechanism.
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Affiliation(s)
- Kathleen M Clark
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Nadia Fedoriw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642
| | - Mark E Dumont
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642.,Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
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118
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Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Bonvin AMJJ, Milner JJ, Kelly SM, Byron O, Smith BO, Walker D. Structure of the bacterial plant-ferredoxin receptor FusA. Nat Commun 2016; 7:13308. [PMID: 27796364 PMCID: PMC5095587 DOI: 10.1038/ncomms13308] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/21/2016] [Indexed: 01/18/2023] Open
Abstract
Iron is a limiting nutrient in bacterial infection putting it at the centre of an evolutionary arms race between host and pathogen. Gram-negative bacteria utilize TonB-dependent outer membrane receptors to obtain iron during infection. These receptors acquire iron either in concert with soluble iron-scavenging siderophores or through direct interaction and extraction from host proteins. Characterization of these receptors provides invaluable insight into pathogenesis. However, only a subset of virulence-related TonB-dependent receptors have been currently described. Here we report the discovery of FusA, a new class of TonB-dependent receptor, which is utilized by phytopathogenic Pectobacterium spp. to obtain iron from plant ferredoxin. Through the crystal structure of FusA we show that binding of ferredoxin occurs through specialized extracellular loops that form extensive interactions with ferredoxin. The function of FusA and the presence of homologues in clinically important pathogens suggests that small iron-containing proteins represent an iron source for bacterial pathogens. Many bacteria use TonB-dependent outer membrane receptors to scavenge iron from their host during infection. Here, the authors report on the structure and function of FusA, which is a bacterial receptor that is used to obtain iron from plants.
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Affiliation(s)
- Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.,Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, UK.,Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3804, Australia
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Khedidja Mosbahi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Aleksander W Roszak
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Joel J Milner
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Brian O Smith
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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119
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Baumlova A, Gregor J, Boura E. The structural basis for calcium inhibition of lipid kinase PI4K IIalpha and comparison with the apo state. Physiol Res 2016; 65:987-993. [PMID: 27539108 DOI: 10.33549/physiolres.933344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PI4K IIalpha is a critical enzyme for the maintenance of Golgi and is also known to function in the synaptic vesicles. The product of its catalytical function, phosphatidylinositol 4-phosphate (PI4P), is an important lipid molecule because it is a hallmark of the Golgi and TGN, is directly recognized by many proteins and also serves as a precursor molecule for synthesis of higher phosphoinositides. Here, we report crystal structures of PI4K IIalpha enzyme in the apo-state and inhibited by calcium. The apo-structure reveals a surprising rigidity of the active site residues important for catalytic activity. The structure of calcium inhibited kinase reveals how calcium locks ATP in the active site.
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Affiliation(s)
- A Baumlova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
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120
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Sooriyaarachchi S, Chofor R, Risseeuw MDP, Bergfors T, Pouyez J, Dowd CS, Maes L, Wouters J, Jones TA, Van Calenbergh S, Mowbray SL. Targeting an Aromatic Hotspot in Plasmodium falciparum
1-Deoxy-d
-xylulose-5-phosphate Reductoisomerase with β-Arylpropyl Analogues of Fosmidomycin. ChemMedChem 2016; 11:2024-36. [DOI: 10.1002/cmdc.201600249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/09/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Sanjeewani Sooriyaarachchi
- Science for Life Laboratory; Department of Cell and Molecular Biology; Uppsala University; Biomedical Center; Box 596 751 24 Uppsala Sweden
| | - René Chofor
- Laboratory for Medicinal Chemistry (FFW); Gent University; Ottergemsesteenweg 460 9000 Gent Belgium
| | - Martijn D. P. Risseeuw
- Laboratory for Medicinal Chemistry (FFW); Gent University; Ottergemsesteenweg 460 9000 Gent Belgium
| | - Terese Bergfors
- Science for Life Laboratory; Department of Cell and Molecular Biology; Uppsala University; Biomedical Center; Box 596 751 24 Uppsala Sweden
| | - Jenny Pouyez
- Department of Chemistry; University of Namur; Rue de Bruxelles 61 5000 Namur Belgium
| | - Cynthia S. Dowd
- Department of Chemistry; George Washington University; Washington DC 20052 USA
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH); University of Antwerp; Universiteitsplein 1 2610 Antwerp Belgium
| | - Johan Wouters
- Department of Chemistry; University of Namur; Rue de Bruxelles 61 5000 Namur Belgium
| | - T. Alwyn Jones
- Science for Life Laboratory; Department of Cell and Molecular Biology; Uppsala University; Biomedical Center; Box 596 751 24 Uppsala Sweden
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW); Gent University; Ottergemsesteenweg 460 9000 Gent Belgium
| | - Sherry L. Mowbray
- Science for Life Laboratory; Department of Cell and Molecular Biology; Uppsala University; Biomedical Center; Box 596 751 24 Uppsala Sweden
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121
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Structure of the host-recognition device of Staphylococcus aureus phage ϕ11. Sci Rep 2016; 6:27581. [PMID: 27282779 PMCID: PMC4901313 DOI: 10.1038/srep27581] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/17/2016] [Indexed: 12/16/2022] Open
Abstract
Phages play key roles in the pathogenicity and adaptation of the human pathogen Staphylococcus aureus. However, little is known about the molecular recognition events that mediate phage adsorption to the surface of S. aureus. The lysogenic siphophage ϕ11 infects S. aureus SA113. It was shown previously that ϕ11 requires α- or β-N-acetylglucosamine (GlcNAc) moieties on cell wall teichoic acid (WTA) for adsorption. Gp45 was identified as the receptor binding protein (RBP) involved in this process and GlcNAc residues on WTA were found to be the key component of the ϕ11 receptor. Here we report the crystal structure of the RBP of ϕ11, which assembles into a large, multidomain homotrimer. Each monomer contains a five-bladed propeller domain with a cavity that could accommodate a GlcNAc moiety. An electron microscopy reconstruction of the ϕ11 host adhesion component, the baseplate, reveals that six RBP trimers are assembled around the baseplate core. The Gp45 and baseplate structures provide insights into the overall organization and molecular recognition process of the phage ϕ11 tail. This assembly is conserved among most glycan-recognizing Siphoviridae, and the RBP orientation would allow host adhesion and infection without an activation step.
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122
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Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State. Structure 2016; 24:1120-9. [PMID: 27238969 DOI: 10.1016/j.str.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/14/2016] [Accepted: 04/09/2016] [Indexed: 01/05/2023]
Abstract
Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, manifested as quaternary reorganization into a high molecular weight (HMW) form. Acidification, for example, causes dodecameric rings of human peroxiredoxin 3 (HsPrx3) to stack into long helical filaments. In this work, a 4.1-Å resolution structure of low-pH-instigated helical filaments was elucidated, showing a locally unfolded active site and partially folded C terminus. A 2.8-Å crystal structure of HsPrx3 was determined at pH 8.5 under reducing conditions, wherein dodecameric rings are arranged as a short stack, with symmetry similar to low-pH filaments. In contrast to previous observations, the crystal structure displays both a fully folded active site and ordered C terminus, suggesting that the HsPrx3 HMW form maintains catalytic activity. We propose a new role for the HMW form as a self-chaperoning assembly maintaining HsPrx3 function under stress.
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123
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Chataigner L, Guo J, Erskine PT, Coker AR, Wood SP, Gombos Z, Cooper JB. Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site. Acta Crystallogr F Struct Biol Commun 2016; 72:276-81. [PMID: 27050260 PMCID: PMC4822983 DOI: 10.1107/s2053230x16003526] [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: 12/21/2015] [Accepted: 02/29/2016] [Indexed: 11/11/2022] Open
Abstract
Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg(2+) and Ca(2+), while EF-3 is likely to bind only Ca(2+). The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd(3+) in the presence of trace Ca(2+), EF-1 was shown to become fully occupied by Gd(3+) ions, while the other two sites remain fully occupied by Ca(2+). The structure of the Gd(3+)-calexcitin complex has been refined to an R factor of 21.5% and an Rfree of 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca(2+)-binding site with the lowest selectivity for Ca(2+), and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.
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Affiliation(s)
- Lucas Chataigner
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Jingxu Guo
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Peter T. Erskine
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
| | - Alun R. Coker
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Steve P. Wood
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Zoltan Gombos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Jonathan B. Cooper
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
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124
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Gorrec F. Protein crystallization screens developed at the MRC Laboratory of Molecular Biology. Drug Discov Today 2016; 21:819-25. [PMID: 27032894 PMCID: PMC4911435 DOI: 10.1016/j.drudis.2016.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/04/2016] [Accepted: 03/08/2016] [Indexed: 12/12/2022]
Abstract
In order to solve increasingly challenging protein structures with crystallography, crystallization reagents and screen formulations are regularly investigated. Here, we briefly describe 96-condition screens developed at the MRC Laboratory of Molecular Biology: the LMB sparse matrix screen, Pi incomplete factorial screens, the MORPHEUS grid screens and the ANGSTROM optimization screen. In this short review, we also discuss the difficulties and advantages associated with the development of protein crystallization screens.
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Affiliation(s)
- Fabrice Gorrec
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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125
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Tongsook C, Uhl MK, Jankowitsch F, Mack M, Gruber K, Macheroux P. Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-d-riboflavin to the antibiotic roseoflavin. FEBS J 2016; 283:1531-49. [PMID: 26913589 PMCID: PMC4982073 DOI: 10.1111/febs.13690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/26/2016] [Accepted: 02/18/2016] [Indexed: 11/28/2022]
Abstract
N,N‐8‐demethyl‐8‐amino‐d‐riboflavin dimethyltransferase (RosA) catalyses the final dimethylation of 8‐demethyl‐8‐amino‐d‐riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study, we solved the X‐ray structure of RosA, and determined the binding properties of substrates and products. Moreover, we used steady‐state and rapid reaction kinetic studies to obtain detailed information on the reaction mechanism. The structure of RosA was found to be similar to that of previously described S‐adenosylmethionine (SAM)‐dependent methyltransferases, featuring two domains: a mainly α‐helical ‘orthogonal bundle’ and a Rossmann‐like domain (α/β twisted open sheet). Bioinformatics studies and molecular modelling enabled us to predict the potential SAM and AF binding sites in RosA, suggesting that both substrates, AF and SAM, bind independently to their respective binding pocket. This finding was confirmed by kinetic experiments that demonstrated a random‐order ‘bi‐bi’ reaction mechanism. Furthermore, we determined the dissociation constants for substrates and products by either isothermal titration calorimetry or UV/Vis absorption spectroscopy, revealing that both products, RoF and S‐adenosylhomocysteine (SAH), bind more tightly to RosA compared with the substrates, AF and SAM. This suggests that RosA may contribute to roseoflavin resistance in S. davawensis. The tighter binding of products is also reflected by the results of inhibition experiments, in which RoF and SAH behave as competitive inhibitors for AF and SAM, respectively. We also showed that formation of a ternary complex of RosA, RoF and SAH (or SAM) leads to drastic spectral changes that are indicative of a hydrophobic environment. Database Structural data are available in the Protein Data Bank under accession number 4D7K.
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Affiliation(s)
| | - Michael K Uhl
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Frank Jankowitsch
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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126
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Busby JN, Lott JS, Panjikar S. Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:182-91. [PMID: 26894666 DOI: 10.1107/s2059798315023566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022]
Abstract
The B and C proteins from the ABC toxin complex of Yersinia entomophaga form a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12 data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used in Auto-Rickshaw for multiple rounds of autobuilding and MRSAD.
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Affiliation(s)
- Jason Nicholas Busby
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Santosh Panjikar
- MX, Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
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127
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Bokhove M, Sadat Al Hosseini H, Saito T, Dioguardi E, Gegenschatz-Schmid K, Nishimura K, Raj I, de Sanctis D, Han L, Jovine L. Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins. J Struct Biol 2016; 194:1-7. [PMID: 26850170 PMCID: PMC4771870 DOI: 10.1016/j.jsb.2016.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 01/19/2023]
Abstract
We present a strategy to obtain milligrams of highly post-translationally modified eukaryotic proteins, transiently expressed in mammalian cells as rigid or cleavable fusions with a mammalianized version of bacterial maltose-binding protein (mMBP). This variant was engineered to combine mutations that enhance MBP solubility and affinity purification, as well as provide crystal-packing interactions for increased crystallizability. Using this cell type-independent approach, we could increase the expression of secreted and intracellular human proteins up to 200-fold. By molecular replacement with MBP, we readily determined five novel high-resolution structures of rigid fusions of targets that otherwise defied crystallization.
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Affiliation(s)
- Marcel Bokhove
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Hamed Sadat Al Hosseini
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Takako Saito
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Elisa Dioguardi
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Katharina Gegenschatz-Schmid
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Kaoru Nishimura
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Isha Raj
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | | | - Ling Han
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden
| | - Luca Jovine
- Karolinska Institutet, Department of Biosciences and Nutrition & Center for Innovative Medicine, Huddinge, Sweden.
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128
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Tarique KF, Devi S, Abdul Rehman SA, Gourinath S. Crystal structure of HINT from Helicobacter pylori. Acta Crystallogr F Struct Biol Commun 2016; 72:42-8. [PMID: 26750483 PMCID: PMC4708049 DOI: 10.1107/s2053230x15023316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/04/2015] [Indexed: 11/10/2022] Open
Abstract
Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom.
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Affiliation(s)
- K. F. Tarique
- School of Life Science, Jawaharlal Nehru University, New Delhi, Delhi 110 067, India
| | - S. Devi
- School of Life Science, Jawaharlal Nehru University, New Delhi, Delhi 110 067, India
| | - S. A. Abdul Rehman
- School of Life Science, Jawaharlal Nehru University, New Delhi, Delhi 110 067, India
| | - S. Gourinath
- School of Life Science, Jawaharlal Nehru University, New Delhi, Delhi 110 067, India
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129
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Arena de Souza V, Scott DJ, Nettleship JE, Rahman N, Charlton MH, Walsh MA, Owens RJ. Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1. PLoS One 2015; 10:e0143919. [PMID: 26657071 PMCID: PMC4676782 DOI: 10.1371/journal.pone.0143919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/11/2015] [Indexed: 11/25/2022] Open
Abstract
Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentically glycosylated and aglycosylated hCES1, generated by mutating asparagine 79 to glutamine, were produced in human embryonic kidney cells. Purified enzymes were shown to be predominantly trimeric in solution by analytical ultracentrifugation. The purified aglycosylated enzyme was found to be more active than glycosylated hCES1 and analysis of enzyme kinetics revealed that both enzymes exhibit positive cooperativity. Crystal structures of hCES1 a catalytically inactive mutant (S221A) and the aglycosylated enzyme were determined in the absence of any ligand or substrate to high resolutions (1.86 Å, 1.48 Å and 2.01 Å, respectively). Superposition of all three structures showed only minor conformational differences with a root mean square deviations of around 0.5 Å over all Cα positions. Comparison of the active sites of these un-liganded enzymes with the structures of hCES1-ligand complexes showed that side-chains of the catalytic triad were pre-disposed for substrate binding. Overall the results indicate that preventing N-glycosylation of hCES1 does not significantly affect the structure or activity of the enzyme.
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Affiliation(s)
- Victoria Arena de Souza
- UK OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - David J. Scott
- The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
| | - Joanne E. Nettleship
- UK OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Nahid Rahman
- UK OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Michael H. Charlton
- Chroma Therapeutics Ltd., 93 Innovation Drive Milton Park, Abingdon, United Kingdom
| | - Martin A. Walsh
- The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
- * E-mail: (MAW); (RJO)
| | - Raymond J. Owens
- UK OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxfordshire, United Kingdom
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
- * E-mail: (MAW); (RJO)
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130
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Booth MPS, Kosmopoulou M, Poirel L, Nordmann P, Spencer J. Crystal Structure of DIM-1, an Acquired Subclass B1 Metallo-β-Lactamase from Pseudomonas stutzeri. PLoS One 2015; 10:e0140059. [PMID: 26451836 PMCID: PMC4599830 DOI: 10.1371/journal.pone.0140059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/20/2015] [Indexed: 11/18/2022] Open
Abstract
Metallo-β-lactamases (MBLs) hydrolyze almost all classes of β-lactam antibiotic, including carbapenems—currently first choice drugs for opportunistic infections by Gram-negative bacterial pathogens. MBL inhibitor development is complicated by the diversity within this group of enzymes, and by the appearance of new enzymes that continue to be identified both as chromosomal genes and on mobile genetic elements. One such newly discovered MBL is DIM-1, a mobile enzyme originally discovered in the opportunist pathogen Pseudomonas stutzeri but subsequently identified in other species and locations. DIM-1 is a subclass B1 MBL more closely related to the TMB-1, GIM-1 and IMP enzymes than to other clinically encountered MBLs such as VIM and NDM; and possesses Arg, rather than the more usual Lys, at position 224 in the putative substrate binding site. Here we report the crystallization and structure determination of DIM-1. DIM-1 possesses a binuclear metal center with a 5 (rather than the more usual 4) co-ordinate tri-histidine (Zn1) site and both 4- and 5-co-ordinate Cys-His-Asp- (Zn2) sites observed in the two molecules of the crystallographic asymmetric unit. These data indicate a degree of variability in metal co-ordination geometry in the DIM-1 active site, as well as facilitating inclusion of DIM-1 in structure-based MBL inhibitor discovery programmes.
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Affiliation(s)
- Michael P. S. Booth
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Magda Kosmopoulou
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Rue Albert Gockel 3, CH-1700, Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Rue Albert Gockel 3, CH-1700, Fribourg, Switzerland
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
- * E-mail:
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131
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Huculeci R, Garcia-Pino A, Buts L, Lenaerts T, van Nuland N. Structural insights into the intertwined dimer of fyn SH2. Protein Sci 2015; 24:1964-78. [PMID: 26384592 DOI: 10.1002/pro.2806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/13/2015] [Accepted: 09/16/2015] [Indexed: 01/01/2023]
Abstract
Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand.
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Affiliation(s)
- Radu Huculeci
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Lieven Buts
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Tom Lenaerts
- MLG, Département d'Informatique, Université Libre de Bruxelles, Brussels, Belgium.,AI-Lab,Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Brussels, Belgium.,Interuniversity Institute of Bioinformatics Brussels (IB2), ULB-VUB, Brussels, Belgium
| | - Nico van Nuland
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
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132
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van der Beek SL, Le Breton Y, Ferenbach AT, Chapman RN, van Aalten DMF, Navratilova I, Boons GJ, McIver KS, van Sorge NM, Dorfmueller HC. GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD). Mol Microbiol 2015; 98:946-62. [PMID: 26278404 PMCID: PMC4832382 DOI: 10.1111/mmi.13169] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 12/29/2022]
Abstract
The sugar nucleotide dTDP‐L‐rhamnose is critical for the biosynthesis of the Group A Carbohydrate, the molecular signature and virulence determinant of the human pathogen Group A Streptococcus (GAS). The final step of the four‐step dTDP‐L‐rhamnose biosynthesis pathway is catalyzed by dTDP‐4‐dehydrorhamnose reductases (RmlD). RmlD from the Gram‐negative bacterium Salmonella is the only structurally characterized family member and requires metal‐dependent homo‐dimerization for enzymatic activity. Using a biochemical and structural biology approach, we demonstrate that the only RmlD homologue from GAS, previously renamed GacA, functions in a novel monomeric manner. Sequence analysis of 213 Gram‐negative and Gram‐positive RmlD homologues predicts that enzymes from all Gram‐positive species lack a dimerization motif and function as monomers. The enzymatic function of GacA was confirmed through heterologous expression of gacA in a S. mutans rmlD knockout, which restored attenuated growth and aberrant cell division. Finally, analysis of a saturated mutant GAS library using Tn‐sequencing and generation of a conditional‐expression mutant identified gacA as an essential gene for GAS. In conclusion, GacA is an essential monomeric enzyme in GAS and representative of monomeric RmlD enzymes in Gram‐positive bacteria and a subset of Gram‐negative bacteria. These results will help future screens for novel inhibitors of dTDP‐L‐rhamnose biosynthesis.
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Affiliation(s)
- Samantha L van der Beek
- University Medical Center Utrecht, Medical Microbiology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, 3124 Biosciences Research Building, College Park, MD 20742, USA
| | - Andrew T Ferenbach
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Robert N Chapman
- Complex Carbohydrate Research Center, Department of Chemistry, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Daan M F van Aalten
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Iva Navratilova
- Division of Biological Chemistry and Drug Discovery, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, Department of Chemistry, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, 3124 Biosciences Research Building, College Park, MD 20742, USA
| | - Nina M van Sorge
- University Medical Center Utrecht, Medical Microbiology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK.,Rutherford Appleton Laboratory, Research Complex at Harwell, OX11 0FA, Didcot, UK
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133
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Mpakali A, Giastas P, Mathioudakis N, Mavridis IM, Saridakis E, Stratikos E. Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2. J Biol Chem 2015; 290:26021-32. [PMID: 26381406 DOI: 10.1074/jbc.m115.685909] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases process antigenic peptide precursors to generate epitopes for presentation by MHC class I molecules and help shape the antigenic peptide repertoire and cytotoxic T-cell responses. To perform this function, ER aminopeptidases have to recognize and process a vast variety of peptide sequences. To understand how these enzymes recognize substrates, we determined crystal structures of ER aminopeptidase 2 (ERAP2) in complex with a substrate analogue and a peptidic product to 2.5 and 2.7 Å, respectively, and compared them to the apo-form structure determined to 3.0 Å. The peptides were found within the internal cavity of the enzyme with no direct access to the outside solvent. The substrate analogue extends away from the catalytic center toward the distal end of the internal cavity, making interactions with several shallow pockets along the path. A similar configuration was evident for the peptidic product, although decreasing electron density toward its C terminus indicated progressive disorder. Enzymatic analysis confirmed that visualized interactions can either positively or negatively impact in vitro trimming rates. Opportunistic side-chain interactions and lack of deep specificity pockets support a limited-selectivity model for antigenic peptide processing by ERAP2. In contrast to proposed models for the homologous ERAP1, no specific recognition of the peptide C terminus by ERAP2 was evident, consistent with functional differences in length selection and self-activation between these two enzymes. Our results suggest that ERAP2 selects substrates by sequestering them in its internal cavity and allowing opportunistic interactions to determine trimming rates, thus combining substrate permissiveness with sequence bias.
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Affiliation(s)
- Anastasia Mpakali
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Petros Giastas
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Nikolas Mathioudakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Irene M Mavridis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Emmanuel Saridakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Efstratios Stratikos
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
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134
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Mpakali A, Saridakis E, Harlos K, Zhao Y, Papakyriakou A, Kokkala P, Georgiadis D, Stratikos E. Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing. THE JOURNAL OF IMMUNOLOGY 2015; 195:2842-51. [PMID: 26259583 DOI: 10.4049/jimmunol.1501103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/13/2015] [Indexed: 12/12/2022]
Abstract
Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understood. In this work, we report the structure of insulin-regulated aminopeptidase, an enzyme that prepares antigenic epitopes for cross-presentation in dendritic cells, in complex with an antigenic peptide precursor analog. Insulin-regulated aminopeptidase is found in a semiclosed conformation with an extended internal cavity with limited access to the solvent. The N-terminal moiety of the peptide is located at the active site, positioned optimally for catalysis, whereas the C-terminal moiety of the peptide is stabilized along the extended internal cavity lodged between domains II and IV. Hydrophobic interactions and shape complementarity enhance peptide affinity beyond the catalytic site and support a limited selectivity model for antigenic peptide selection that may underlie the generation of complex immunopeptidomes.
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Affiliation(s)
- Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Emmanuel Saridakis
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom; and
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom; and
| | | | - Paraskevi Kokkala
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece; Department of Chemistry, University of Athens, Athens 15771, Greece
| | | | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece;
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135
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Chaikuad A, Knapp S, von Delft F. Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1627-39. [PMID: 26249344 PMCID: PMC4528798 DOI: 10.1107/s1399004715007968] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/22/2015] [Indexed: 11/10/2022]
Abstract
The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.
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Affiliation(s)
- Apirat Chaikuad
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Building N240 Room 3.03, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Frank von Delft
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
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136
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Gorrec F. The MORPHEUS II protein crystallization screen. Acta Crystallogr F Struct Biol Commun 2015; 71:831-7. [PMID: 26144227 PMCID: PMC4498703 DOI: 10.1107/s2053230x1500967x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/19/2015] [Indexed: 11/10/2022] Open
Abstract
High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.
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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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137
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Lountos GT, Austin BP, Tropea JE, Waugh DS. Structure of human dual-specificity phosphatase 7, a potential cancer drug target. Acta Crystallogr F Struct Biol Commun 2015; 71:650-6. [PMID: 26057789 PMCID: PMC4461324 DOI: 10.1107/s2053230x1500504x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 03/12/2015] [Indexed: 11/10/2022] Open
Abstract
Human dual-specificity phosphatase 7 (DUSP7/Pyst2) is a 320-residue protein that belongs to the mitogen-activated protein kinase phosphatase (MKP) subfamily of dual-specificity phosphatases. Although its precise biological function is still not fully understood, previous reports have demonstrated that DUSP7 is overexpressed in myeloid leukemia and other malignancies. Therefore, there is interest in developing DUSP7 inhibitors as potential therapeutic agents, especially for cancer. Here, the purification, crystallization and structure determination of the catalytic domain of DUSP7 (Ser141-Ser289/C232S) at 1.67 Å resolution are reported. The structure described here provides a starting point for structure-assisted inhibitor-design efforts and adds to the growing knowledge base of three-dimensional structures of the dual-specificity phosphatase family.
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Affiliation(s)
- George T. Lountos
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - Brian P. Austin
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
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138
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Rogala KB, Dynes NJ, Hatzopoulos GN, Yan J, Pong SK, Robinson CV, Deane CM, Gönczy P, Vakonakis I. The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation. eLife 2015; 4:e07410. [PMID: 26023830 PMCID: PMC4471805 DOI: 10.7554/elife.07410] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/28/2015] [Indexed: 12/21/2022] Open
Abstract
Centrioles are microtubule-based organelles crucial for cell division, sensing and motility. In Caenorhabditis elegans, the onset of centriole formation requires notably the proteins SAS-5 and SAS-6, which have functional equivalents across eukaryotic evolution. Whereas the molecular architecture of SAS-6 and its role in initiating centriole formation are well understood, the mechanisms by which SAS-5 and its relatives function is unclear. Here, we combine biophysical and structural analysis to uncover the architecture of SAS-5 and examine its functional implications in vivo. Our work reveals that two distinct self-associating domains are necessary to form higher-order oligomers of SAS-5: a trimeric coiled coil and a novel globular dimeric Implico domain. Disruption of either domain leads to centriole duplication failure in worm embryos, indicating that large SAS-5 assemblies are necessary for function in vivo. DOI:http://dx.doi.org/10.7554/eLife.07410.001 Most animal cells contain structures known as centrioles. Typically, a cell that is not dividing contains a pair of centrioles. But when a cell prepares to divide, the centrioles are duplicated. The two pairs of centrioles then organize the scaffolding that shares the genetic material equally between the newly formed cells at cell division. Centriole assembly is tightly regulated and abnormalities in this process can lead to developmental defects and cancer. Centrioles likely contain several hundred proteins, but only a few of these are strictly needed for centriole assembly. New centrioles usually assemble from a cartwheel-like arrangement of proteins, which includes a protein called SAS-6. In the worm Caenorhabditis elegans, SAS-6 associates with another protein called SAS-5. This interaction is essential for centrioles to form, but the reason behind this is not clearly understood. Now, Rogala et al. have used a range of techniques including X-ray crystallography, biophysics and studies of worm embryos to investigate the role of SAS-5 in C. elegans. These experiments revealed that SAS-5 proteins can interact with each other, via two regions of each protein termed a ‘coiled-coil’ and a previously unrecognized ‘Implico domain’. These regions drive the formation of assemblies that contain multiple SAS-5 proteins. Next, Rogala et al. asked whether SAS-5 assemblies are important for centriole duplication. Mutant worm embryos, in which SAS-5 proteins could not interact with one another, failed to form new centrioles. This resulted in defects with cell division. An independent study by Cottee, Muschalik et al. obtained similar results and found that the fruit fly equivalent of SAS-5, called Ana2, can also self-associate and this activity is required for centriole duplication. Further work is now needed to understand how SAS-5 and SAS-6 work with each other to form the initial framework at the core of centrioles. DOI:http://dx.doi.org/10.7554/eLife.07410.002
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Affiliation(s)
- Kacper B Rogala
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Nicola J Dynes
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | | | - Jun Yan
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Sheng Kai Pong
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Ioannis Vakonakis
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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139
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Needle D, Lountos GT, Waugh DS. Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. ACTA ACUST UNITED AC 2015; 71:1102-11. [PMID: 25945576 PMCID: PMC4427198 DOI: 10.1107/s1399004715003521] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/19/2015] [Indexed: 11/21/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS‐CoV) is a highly pathogenic virus that causes severe respiratory illness accompanied by multi‐organ dysfunction, resulting in a case fatality rate of approximately 40%. As found in other coronaviruses, the majority of the positive‐stranded RNA MERS‐CoV genome is translated into two polyproteins, one created by a ribosomal frameshift, that are cleaved at three sites by a papain‐like protease and at 11 sites by a 3C‐like protease (3CLpro). Since 3CLpro is essential for viral replication, it is a leading candidate for therapeutic intervention. To accelerate the development of 3CLpro inhibitors, three crystal structures of a catalytically inactive variant (C148A) of the MERS‐CoV 3CLpro enzyme were determined. The aim was to co‐crystallize the inactive enzyme with a peptide substrate. Fortuitously, however, in two of the structures the C‐terminus of one protomer is bound in the active site of a neighboring molecule, providing a snapshot of an enzyme–product complex. In the third structure, two of the three protomers in the asymmetric unit form a homodimer similar to that of SARS‐CoV 3CLpro; however, the third protomer adopts a radically different conformation that is likely to correspond to a crystallographic monomer, indicative of substantial structural plasticity in the enzyme. The results presented here provide a foundation for the structure‐based design of small‐molecule inhibitors of the MERS‐CoV 3CLpro enzyme.
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Affiliation(s)
- Danielle Needle
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - George T Lountos
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
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140
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Khurshid S, Govada L, El-Sharif HF, Reddy SM, Chayen NE. Automating the application of smart materials for protein crystallization. ACTA ACUST UNITED AC 2015; 71:534-40. [PMID: 25760603 PMCID: PMC4356364 DOI: 10.1107/s1399004714027643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022]
Abstract
The first semi-liquid, non-protein nucleating agent for automated protein crystallization trials is described. This ‘smart material’ is demonstrated to induce crystal growth and will provide a simple, cost-effective tool for scientists in academia and industry. The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as ‘smart materials’) for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials.
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Affiliation(s)
- Sahir Khurshid
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
| | - Lata Govada
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
| | - Hazim F El-Sharif
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, England
| | - Subrayal M Reddy
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, England
| | - Naomi E Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
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141
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Hadži S, Garcia-Pino A, Gerdes K, Lah J, Loris R. Crystallization of two operator complexes from the Vibrio cholerae HigBA2 toxin-antitoxin module. Acta Crystallogr F Struct Biol Commun 2015; 71:226-33. [PMID: 25664801 PMCID: PMC4321481 DOI: 10.1107/s2053230x15000746] [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: 11/05/2014] [Accepted: 01/13/2015] [Indexed: 11/11/2022] Open
Abstract
The HigA2 antitoxin and the HigBA2 toxin-antitoxin complex from Vibrio cholerae were crystallized in complex with their operator box. Screening of 22 different DNA duplexes led to two crystal forms of HigA2 complexes and one crystal form of a HigBA2 complex. Crystals of HigA2 in complex with a 17 bp DNA duplex belong to space group P3221, with unit-cell parameters a = b = 94.0, c = 123.7 Å, and diffract to 2.3 Å resolution. The second form corresponding to HigA2 in complex with a 19 bp duplex belong to space group P43212 and only diffract to 3.45 Å resolution. Crystals of the HigBA2 toxin-antitoxin were obtained in complex with a 31 bp duplex and belonged to space group P41212, with unit-cell parameters a = b = 113.6, c = 121.1 Å. They diffract to 3.3 Å resolution.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ascerceva 5, 1000 Ljubljana, Slovenia
| | - Abel Garcia-Pino
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ascerceva 5, 1000 Ljubljana, Slovenia
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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142
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Ting YT, Batot G, Baker EN, Young PG. Expression, purification and crystallization of a membrane-associated, catalytically active type I signal peptidase from Staphylococcus aureus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:61-5. [PMID: 25615971 DOI: 10.1107/s2053230x1402603x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 11/27/2014] [Indexed: 04/09/2023]
Abstract
Staphylococcus aureus infections are becoming increasingly difficult to treat as they rapidly develop resistance to existing antibiotics. Bacterial type I signal peptidases are membrane-associated, cell-surface serine proteases with a unique catalytic mechanism that differs from that of eukaryotic endoplasmic reticulum signal peptidases. They are thus potential antimicrobial targets. S. aureus has a catalytically active type I signal peptidase, SpsB, that is essential for cell viability. To elucidate its structure, the spsB gene from S. aureus Newman strain was cloned and overexpressed in Escherichia coli. After exploring many different protein-modification constructs, SpsB was expressed as a fusion protein with maltose-binding protein and crystallized by hanging-drop vapour diffusion. The crystals belonged to the monoclinic space group P2(1) and diffracted to 2.05 Å resolution. The crystal structure of SpsB is anticipated to provide structural insight into Gram-positive signal peptidases and to aid in the development of antibacterial agents that target type I signal peptidases.
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Affiliation(s)
- Yi Tian Ting
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Gaëlle Batot
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Paul G Young
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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143
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Lagautriere T, Bashiri G, Baker EN. Use of a "silver bullet" to resolve crystal lattice dislocation disorder: a cobalamin complex of Δ1-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis. J Struct Biol 2014; 189:153-7. [PMID: 25557497 DOI: 10.1016/j.jsb.2014.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/26/2014] [Accepted: 12/26/2014] [Indexed: 11/26/2022]
Abstract
The use of small molecules as "silver bullets" that can bind to generate crosslinks between protein molecules has been advanced as a powerful means of enhancing success in protein crystallization (McPherson and Cudney, 2006). We have explored this approach in attempts to overcome an order-disorder phenomenon that complicated the structural analysis of the enzyme Δ(1)-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis (P5CDH, Mtb-PruA). Using the Silver Bullets Bio screen, we obtained new crystal packing using cobalamin as a co-crystallization agent. This crystal form did not display the order-disorder phenomenon previously encountered. Solution of the crystal structure showed that cobalamin molecules are present in the crystal contacts. Although the cobalamin binding probably does not have physiological relevance, it reflects similarities in the nucleotide-binding region of Mtb-PruA, with the nucleotide loop of cobalamin sharing the binding site for the adenine moiety of NAD(+).
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Affiliation(s)
- Thomas Lagautriere
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Ghader Bashiri
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Edward N Baker
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand.
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144
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Badarau A, Rouha H, Malafa S, Logan DT, Håkansson M, Stulik L, Dolezilkova I, Teubenbacher A, Gross K, Maierhofer B, Weber S, Jägerhofer M, Hoffman D, Nagy E. Structure-function analysis of heterodimer formation, oligomerization, and receptor binding of the Staphylococcus aureus bi-component toxin LukGH. J Biol Chem 2014; 290:142-56. [PMID: 25371205 DOI: 10.1074/jbc.m114.598110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The bi-component leukocidins of Staphylococcus aureus are important virulence factors that lyse human phagocytic cells and contribute to immune evasion. The γ-hemolysins (HlgAB and HlgCB) and Panton-Valentine leukocidin (PVL or LukSF) were shown to assemble from soluble subunits into membrane-bound oligomers on the surface of target cells, creating barrel-like pore structures that lead to cell lysis. LukGH is the most distantly related member of this toxin family, sharing only 30-40% amino acid sequence identity with the others. We observed that, unlike other leukocidin subunits, recombinant LukH and LukG had low solubility and were unable to bind to target cells, unless both components were present. Using biolayer interferometry and intrinsic tryptophan fluorescence we detected binding of LukH to LukG in solution with an affinity in the low nanomolar range and dynamic light scattering measurements confirmed formation of a heterodimer. We elucidated the structure of LukGH by x-ray crystallography at 2.8-Å resolution. This revealed an octameric structure that strongly resembles that reported for HlgAB, but with important structural differences. Structure guided mutagenesis studies demonstrated that three salt bridges, not found in other bi-component leukocidins, are essential for dimer formation in solution and receptor binding. We detected weak binding of LukH, but not LukG, to the cellular receptor CD11b by biolayer interferometry, suggesting that in common with other members of this toxin family, the S-component has the primary contact role with the receptor. These new insights provide the basis for novel strategies to counteract this powerful toxin and Staphylococcus aureus pathogenesis.
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Affiliation(s)
- Adriana Badarau
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Harald Rouha
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Stefan Malafa
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, S-223 81 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, S-223 81 Lund, Sweden
| | - Lukas Stulik
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Ivana Dolezilkova
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Astrid Teubenbacher
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Karin Gross
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Barbara Maierhofer
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Susanne Weber
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Michaela Jägerhofer
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - David Hoffman
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
| | - Eszter Nagy
- From Arsanis Biosciences, Vienna Biocenter Campus, Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria and
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145
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Stanger FV, Dehio C, Schirmer T. Structure of the N-terminal Gyrase B fragment in complex with ADP⋅Pi reveals rigid-body motion induced by ATP hydrolysis. PLoS One 2014; 9:e107289. [PMID: 25202966 PMCID: PMC4159350 DOI: 10.1371/journal.pone.0107289] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022] Open
Abstract
Type II DNA topoisomerases are essential enzymes that catalyze topological rearrangement of double-stranded DNA using the free energy generated by ATP hydrolysis. Bacterial DNA gyrase is a prototype of this family and is composed of two subunits (GyrA, GyrB) that form a GyrA2GyrB2 heterotetramer. The N-terminal 43-kDa fragment of GyrB (GyrB43) from E. coli comprising the ATPase and the transducer domains has been studied extensively. The dimeric fragment is competent for ATP hydrolysis and its structure in complex with the substrate analog AMPPNP is known. Here, we have determined the remaining conformational states of the enzyme along the ATP hydrolysis reaction path by solving crystal structures of GyrB43 in complex with ADP⋅BeF3, ADP⋅Pi, and ADP. Upon hydrolysis, the enzyme undergoes an obligatory 12° domain rearrangement to accommodate the 1.5 Å increase in distance between the γ- and β-phosphate of the nucleotide within the sealed binding site at the domain interface. Conserved residues from the QTK loop of the transducer domain (also part of the domain interface) couple the small structural change within the binding site with the rigid body motion. The domain reorientation is reflected in a significant 7 Å increase in the separation of the two transducer domains of the dimer that would embrace one of the DNA segments in full-length gyrase. The observed conformational change is likely to be relevant for the allosteric coordination of ATP hydrolysis with DNA binding, cleavage/re-ligation and/or strand passage.
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Affiliation(s)
- Frédéric V. Stanger
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail:
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146
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Boucher LE, Bosch J. Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase. Acta Crystallogr F Struct Biol Commun 2014; 70:1186-92. [PMID: 25195889 PMCID: PMC4157416 DOI: 10.1107/s2053230x14017087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/24/2014] [Indexed: 12/03/2022] Open
Abstract
The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolase has been crystallized in space group P22121, with the biologically relevant tetramer in the asymmetric unit, and the structure has been determined via molecular replacement to a resolution of 2.0 Å. An analysis of the quality of the model and of the differences between the four chains in the asymmetric unit and a comparison between the T. gondii and P. falciparum aldolase structures is presented.
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Affiliation(s)
- Lauren E. Boucher
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
- Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
- Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
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147
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D'Arcy A, Bergfors T, Cowan-Jacob SW, Marsh M. Microseed matrix screening for optimization in protein crystallization: what have we learned? ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1117-26. [PMID: 25195878 DOI: 10.1107/s2053230x14015507] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/02/2014] [Indexed: 11/10/2022]
Abstract
Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems.
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Affiliation(s)
- Allan D'Arcy
- Actelion Pharmaceuticals Ltd, Basel, Switzerland
| | - Terese Bergfors
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandra W Cowan-Jacob
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - May Marsh
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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148
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Roig MB, Löwe J, Chan KL, Beckouët F, Metson J, Nasmyth K. Structure and function of cohesin's Scc3/SA regulatory subunit. FEBS Lett 2014; 588:3692-702. [PMID: 25171859 PMCID: PMC4175184 DOI: 10.1016/j.febslet.2014.08.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022]
Abstract
Crystal structure of cohesin subunit Scc3/SA, showing irregular HEAT-like repeats. Scc3 C-terminal domain binds Scc1, cohesin’s kleisin. Scc1’s Scc3 binding region mapped. Scc3 turns over in G2/M while maintaining cohesin’s association with chromosomes. Scc3 promotes de-acetylation of Smc3 upon Scc1 cleavage.
Sister chromatid cohesion involves entrapment of sister DNAs by a cohesin ring created through association of a kleisin subunit (Scc1) with ATPase heads of Smc1/Smc3 heterodimers. Cohesin’s association with chromatin involves subunits recruited by Scc1: Wapl, Pds5, and Scc3/SA, in addition to Scc2/4 loading complex. Unlike Pds5, Wapl, and Scc2/4, Scc3s are encoded by all eukaryotic genomes. Here, a crystal structure of Scc3 reveals a hook-shaped protein composed of tandem α helices. Its N-terminal domain contains a conserved and essential surface (CES) present even in organisms lacking Pds5, Wapl, and Scc2/4, while its C-terminal domain binds a section of the kleisin Scc1. Scc3 turns over in G2/M while maintaining cohesin’s association with chromosomes and it promotes de-acetylation of Smc3 upon Scc1 cleavage.
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Affiliation(s)
- Maurici B Roig
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Kok-Lung Chan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Frédéric Beckouët
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jean Metson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
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149
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Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1. Sci Rep 2014; 4:5944. [PMID: 25089892 PMCID: PMC4123200 DOI: 10.1038/srep05944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 12/25/2022] Open
Abstract
Influenza A viruses cause the respiratory illness influenza, which can be mild to fatal depending on the strain and host immune response. The flu polymerase acidic (PA), polymerase basic 1 (PB1), and polymerase basic 2 (PB2) proteins comprise the RNA-dependent RNA polymerase complex responsible for viral genome replication. The first crystal structures of the C-terminal domain of PA (PA-CTD) in the absence of PB1-derived peptides show a number of structural changes relative to the previously reported PB1-peptide bound structures. The human A/WSN/1933 (H1N1) and avian A/Anhui1/2013 (H7N9) strain PA-CTD proteins exhibit the same global topology as other strains in the absence of PB1, but differ extensively in the PB1 binding pocket including a widening of the binding groove and the unfolding of a β-turn. Both PA-CTD proteins exhibited a significant increase in thermal stability in the presence of either a PB1-derived peptide or a previously reported inhibitor in differential scanning fluorimetry assays. These structural changes demonstrate plasticity in the PA-PB1 binding interface which may be exploited in the development of novel therapeutics.
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150
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Fairhead M, Shen D, Chan LKM, Lowe ED, Donohoe TJ, Howarth M. Love-Hate ligands for high resolution analysis of strain in ultra-stable protein/small molecule interaction. Bioorg Med Chem 2014; 22:5476-86. [PMID: 25128469 DOI: 10.1016/j.bmc.2014.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 12/19/2022]
Abstract
The pathway of ligand dissociation and how binding sites respond to force are not well understood for any macromolecule. Force effects on biological receptors have been studied through simulation or force spectroscopy, but not by high resolution structural experiments. To investigate this challenge, we took advantage of the extreme stability of the streptavidin-biotin interaction, a paradigm for understanding non-covalent binding as well as a ubiquitous research tool. We synthesized a series of biotin-conjugates having an unchanged strong-binding biotin moiety, along with pincer-like arms designed to clash with the protein surface: 'Love-Hate ligands'. The Love-Hate ligands contained various 2,6-di-ortho aryl groups, installed using Suzuki coupling as the last synthetic step, making the steric repulsion highly modular. We determined binding affinity, as well as solving 1.1-1.6Å resolution crystal structures of streptavidin bound to Love-Hate ligands. Striking distortion of streptavidin's binding contacts was found for these complexes. Hydrogen bonds to biotin's ureido and thiophene rings were preserved for all the ligands, but biotin's valeryl tail was distorted from the classic conformation. Streptavidin's L3/4 loop, normally forming multiple energetically-important hydrogen bonds to biotin, was forced away by clashes with Love-Hate ligands, but Ser45 from L3/4 could adapt to hydrogen-bond to a different part of the ligand. This approach of preparing conflicted ligands represents a direct way to visualize strained biological interactions and test protein plasticity.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Di Shen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Louis K M Chan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Timothy J Donohoe
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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