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Baral PK, Yin J, James MNG. Treatment and prevention strategies for the COVID 19 pandemic: A review of immunotherapeutic approaches for neutralizing SARS-CoV-2. Int J Biol Macromol 2021; 186:490-500. [PMID: 34237371 PMCID: PMC8256663 DOI: 10.1016/j.ijbiomac.2021.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022]
Abstract
Researchers from the world over are working to create prophylactic and therapeutic interventions to combat the COVID-19 global healthcare crisis. The current therapeutic options against the COVID-19 include repurposed drugs aimed at targets other than virus-specific proteins. Antibody-based therapeutics carry a lot of promise, and there are several of these candidates for COVID-19 treatment currently being investigated in the preclinical and clinical research stages around the world. The viral spike protein (S protein) appears to be the main target of antibody development candidates, with the majority being monoclonal antibodies. Several antibody candidates targeting the SARS-CoV-2 S protein include LY-CoV555, REGN-COV2, JS016, TY027, CT-P59, BRII-196, BRII-198 and SCTA01. These neutralizing antibodies will treat COVID-19 and possibly future coronavirus infections. Future studies should focus on effective immune-therapeutics and immunomodulators with the purpose of developing specific, affordable, and cost-effective prophylactic and treatment regimens to fight the COVID-19 globally.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Baral PK, Yin J, Aguzzi A, James MNG. Transition of the prion protein from a structured cellular form (PrP C ) to the infectious scrapie agent (PrP Sc ). Protein Sci 2019; 28:2055-2063. [PMID: 31583788 DOI: 10.1002/pro.3735] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/07/2022]
Abstract
Prion diseases in mammals are caused by a conformational transition of the cellular prion protein from its native conformation (PrPC ) to a pathological isoform called "prion protein scrapie" (PrPSc ). A molecular level of understanding of this conformational transition will be helpful in unveiling the disease etiology. Experimental structural biological techniques (NMR and X-ray crystallography) have been used to unravel the atomic level structural information for the prion and its binding partners. More than one hundred three-dimensional structures of the mammalian prions have been deposited in the protein databank. Structural studies on the prion protein and its structural transitions will deepen our understanding of the molecular basis of prion pathogenesis and will provide valuable guidance for future structure-based drug discovery endeavors.
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Affiliation(s)
- Pravas K Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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3
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James MNG, Yin J, Colazo J, Mosquera F, Vederas JC. A proposal for a substrate-assisted catalytic mechanism for serine peptidases. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318099828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Baral PK, Swayampakula M, Aguzzi A, James MNG. Structural characterization of
POM
6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion. FEBS J 2018; 285:1701-1714. [DOI: 10.1111/febs.14438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/02/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Mridula Swayampakula
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Adriano Aguzzi
- Institute of Neuropathology University of Zurich Switzerland
| | - Michael N. G. James
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
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James MNG, Fraser ME, Khan AR, Parrish JC, Smith WW, Bartlett PA. Structural studies of conformationally-restricted ligands binding to aspartic peptidases. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317099834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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6
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Baral PK, Swayampakula M, Aguzzi A, James MNG. X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins. J Struct Biol 2015; 192:37-47. [PMID: 26320075 DOI: 10.1016/j.jsb.2015.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 02/03/2023]
Abstract
Misfolded prion proteins are the cause of neurodegenerative diseases that affect many mammalian species, including humans. Transmission of the prion diseases poses a considerable public-health risk as a specific prion disease such as bovine spongiform encephalopathy can be transferred to humans and other mammalian species upon contaminant exposure. The underlying mechanism of prion propagation and the species barriers that control cross species transmission has been investigated quite extensively. So far a number of prion strains have been characterized and those have been intimately linked to species-specific infectivity and other pathophysiological manifestations. These strains are encoded by a protein-only agent, and have a high degree of sequence identity across mammalian species. The molecular events that lead to strain differentiation remain elusive. In order to contribute to the understanding of strain differentiation, we have determined the crystal structures of the globular, folded domains of four prion proteins (cow, deer, elk and Syrian hamster) bound to the POM1 antibody fragment Fab. Although the overall structural folds of the mammalian prion proteins remains extremely similar, there are several local structural variations observed in the misfolding-initiator motifs. In additional molecular dynamics simulation studies on these several prion proteins reveal differences in the local fluctuations and imply that these differences have possible roles in the unfolding of the globular domains. These local variations in the structured domains perpetuate diverse patterns of prion misfolding and possibly facilitate the strain selection and adaptation.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Jacobson JM, Yin J, Kitov PI, Mulvey G, Griener TP, James MNG, Armstrong G, Bundle DR. The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor. J Biol Chem 2014; 289:885-94. [PMID: 24225957 PMCID: PMC3887212 DOI: 10.1074/jbc.m113.518886] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/28/2013] [Indexed: 12/31/2022] Open
Abstract
Shiga toxin type 2 (Stx2a) is clinically most closely associated with enterohemorrhagic E. coli O157:H7-mediated hemorrhagic colitis that sometimes progresses to hemolytic-uremic syndrome. The ability to express the toxin has been acquired by other Escherichia coli strains, and outbreaks of food poisoning have caused significant mortality rates as, for example, in the 2011 outbreak in northern Germany. Stx2a, an AB5 toxin, gains entry into human cells via the glycosphingolipid receptor Gb3. We have determined the first crystal structure of a disaccharide analog of Gb3 bound to the B5 pentamer of Stx2a holotoxin. In this Gb3 analog,-GalNAc replaces the terminal-Gal residue. This co-crystal structure confirms previous inferences that two of the primary binding sites identified in theB5 pentamer of Stx1 are also functional in Stx2a. This knowledge provides a rationale for the synthesis and evaluation of heterobifunctional antagonists for E. coli toxins that target Stx2a. Incorporation of GalNAc Gb3 trisaccharide in a heterobifunctional ligand with an attached pyruvate acetal, a ligand for human amyloid P component, and conjugation to poly[acrylamide-co-(3-azidopropylmethacrylamide)] produced a polymer that neutralized Stx2a in a mouse model of Shigatoxemia.
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Affiliation(s)
- Jared M. Jacobson
- From the Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada, and
| | - Pavel I. Kitov
- From the Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - George Mulvey
- Department of Microbiology, Immunology, and Infectious Diseases, Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Tom P. Griener
- Department of Microbiology, Immunology, and Infectious Diseases, Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Michael N. G. James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada, and
| | - Glen Armstrong
- Department of Microbiology, Immunology, and Infectious Diseases, Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - David R. Bundle
- From the Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Baral PK, Swayampakula M, Rout MK, Kav NNV, Spyracopoulos L, Aguzzi A, James MNG. Structural basis of prion inhibition by phenothiazine compounds. Structure 2013; 22:291-303. [PMID: 24373770 DOI: 10.1016/j.str.2013.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/10/2023]
Abstract
Conformational transitions of the cellular form of the prion protein, PrP(C), into an infectious isoform, PrP(Sc), are considered to be central events in the progression of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. Tricyclic phenothiazine compounds exhibit antiprion activity; however, the underlying molecular mechanism of PrP(Sc) inhibition remains elusive. We report the molecular structures of two phenothiazine compounds, promazine and chlorpromazine bound to a binding pocket formed at the intersection of the structured and the unstructured domains of the mouse prion protein. Promazine binding induces structural rearrangement of the unstructured region proximal to β1, through the formation of a "hydrophobic anchor." We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as the C terminus of α2, the α2-α3 loop, as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs induce a PrP(C) isoform that potentially resists oligomerization.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Manoj Kumar Rout
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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9
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Bie H, Yin J, He X, Kermode AR, Goddard-Borger ED, Withers SG, James MNG. Insights into mucopolysaccharidosis I from the structure and action of α-L-iduronidase. Nat Chem Biol 2013; 9:739-45. [PMID: 24036510 PMCID: PMC4954775 DOI: 10.1038/nchembio.1357] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/05/2013] [Indexed: 02/06/2023]
Abstract
Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we crystallized human IDUA produced in an Arabidopsis thaliana cgl mutant. IDUA consists of a TIM barrel domain containing the catalytic site, a β-sandwich domain and a fibronectin-like domain. Structures of IDUA bound to iduronate analogs illustrate the Michaelis complex and reveal a (2,5)B conformation in the glycosyl-enzyme intermediate, which suggest a retaining double displacement reaction involving the nucleophilic Glu299 and the general acid/base Glu182. Unexpectedly, the N-glycan attached to Asn372 interacts with iduronate analogs in the active site and is required for enzymatic activity. Finally, these IDUA structures and biochemical analysis of the disease-relevant P533R mutation have enabled us to correlate the effects of mutations in IDUA to clinical phenotypes.
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Affiliation(s)
- Haiying Bie
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Jiang Yin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Xu He
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Allison R. Kermode
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Ethan D. Goddard-Borger
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z1
| | - Michael N. G. James
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
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Sonati T, Reimann RR, Falsig J, Baral PK, O'Connor T, Hornemann S, Yaganoglu S, Li B, Herrmann US, Wieland B, Swayampakula M, Rahman MH, Das D, Kav N, Riek R, Liberski PP, James MNG, Aguzzi A. The toxicity of antiprion antibodies is mediated by the flexible tail of the prion protein. Nature 2013; 501:102-6. [PMID: 23903654 DOI: 10.1038/nature12402] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Abstract
Prion infections cause lethal neurodegeneration. This process requires the cellular prion protein (PrP(C); ref. 1), which contains a globular domain hinged to a long amino-proximal flexible tail. Here we describe rapid neurotoxicity in mice and cerebellar organotypic cultured slices exposed to ligands targeting the α1 and α3 helices of the PrP(C) globular domain. Ligands included seven distinct monoclonal antibodies, monovalent Fab1 fragments and recombinant single-chain variable fragment miniantibodies. Similar to prion infections, the toxicity of globular domain ligands required neuronal PrP(C), was exacerbated by PrP(C) overexpression, was associated with calpain activation and was antagonized by calpain inhibitors. Neurodegeneration was accompanied by a burst of reactive oxygen species, and was suppressed by antioxidants. Furthermore, genetic ablation of the superoxide-producing enzyme NOX2 (also known as CYBB) protected mice from globular domain ligand toxicity. We also found that neurotoxicity was prevented by deletions of the octapeptide repeats within the flexible tail. These deletions did not appreciably compromise globular domain antibody binding, suggesting that the flexible tail is required to transmit toxic signals that originate from the globular domain and trigger oxidative stress and calpain activation. Supporting this view, various octapeptide ligands were not only innocuous to both cerebellar organotypic cultured slices and mice, but also prevented the toxicity of globular domain ligands while not interfering with their binding. We conclude that PrP(C) consists of two functionally distinct modules, with the globular domain and the flexible tail exerting regulatory and executive functions, respectively. Octapeptide ligands also prolonged the life of mice expressing the toxic PrP(C) mutant, PrP(Δ94-134), indicating that the flexible tail mediates toxicity in two distinct PrP(C)-related conditions. Flexible tail-mediated toxicity may conceivably play a role in further prion pathologies, such as familial Creutzfeldt-Jakob disease in humans bearing supernumerary octapeptides.
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Affiliation(s)
- Tiziana Sonati
- Institute of Neuropathology, University Hospital Zurich, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland
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Swayampakula M, Baral PK, Aguzzi A, Kav NNV, James MNG. The crystal structure of an octapeptide repeat of the prion protein in complex with a Fab fragment of the POM2 antibody. Protein Sci 2013; 22:893-903. [PMID: 23629842 DOI: 10.1002/pro.2270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/09/2022]
Abstract
Prion diseases are progressive, infectious neurodegenerative disorders caused primarily by the misfolding of the cellular prion protein (PrP(c)) into an insoluble, protease-resistant, aggregated isoform termed PrP(sc). In native conditions, PrP(c) has a structured C-terminal domain and a highly flexible N-terminal domain. A part of this N-terminal domain consists of 4-5 repeats of an unusual glycine-rich, eight amino acids long peptide known as the octapeptide repeat (OR) domain. In this article, we successfully report the first crystal structure of an OR of PrP(c) bound to the Fab fragment of the POM2 antibody. The structure was solved at a resolution of 2.3 Å by molecular replacement. Although several studies have previously predicted a β-turn-like structure of the unbound ORs, our structure shows an extended conformation of the OR when bound to a molecule of the POM2 Fab indicating that the bound Fab disrupts any putative native β turn conformation of the ORs. Encouraging results from several recent studies have shown that administering small molecule ligands or antibodies targeting the OR domain of PrP result in arresting the progress of peripheral prion infections both in ex vivo and in in vivo models. This makes the structural study of the interactions of POM2 Fab with the OR domain very important as it would help us to design smaller and tighter binding OR ligands.
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Affiliation(s)
- Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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Baral PK, Wieland B, Swayampakula M, Polymenidou M, Rahman MH, Kav NNV, Aguzzi A, James MNG. Structural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1. Acta Crystallogr D Biol Crystallogr 2012; 68:1501-12. [PMID: 23090399 DOI: 10.1107/s0907444912037328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 08/29/2012] [Indexed: 11/10/2022]
Abstract
Prion diseases are neurodegenerative diseases characterized by the conversion of the cellular prion protein PrP(c) into a pathogenic isoform PrP(sc). Passive immunization with antiprion monoclonal antibodies can arrest the progression of prion diseases. Here, the crystal structure of the Fab fragment of an antiprion monoclonal antibody, POM1, in complex with human prion protein (huPrP(c)) has been determined to 2.4 Å resolution. The prion epitope of POM1 is in close proximity to the epitope recognized by the purportedly therapeutic antibody fragment ICSM18 Fab in complex with huPrP(c). POM1 Fab forms a 1:1 complex with huPrP(c) and the measured K(d) of 4.5 × 10(-7) M reveals moderately strong binding between them. Structural comparisons have been made among three prion-antibody complexes: POM1 Fab-huPrP(c), ICSM18 Fab-huPrP(c) and VRQ14 Fab-ovPrP(c). The prion epitopes recognized by ICSM18 Fab and VRQ14 Fab are adjacent to a prion glycosylation site, indicating possible steric hindrance and/or an altered binding mode to the glycosylated prion protein in vivo. However, both of the glycosylation sites on huPrP(c) are positioned away from the POM1 Fab binding epitope; thus, the binding mode observed in this crystal structure and the binding affinity measured for this antibody are most likely to be the same as those for the native prion protein in vivo.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, School of Translational Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB T6G 2H7, Canada
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Baretta K, Garen C, Yin J, James MNG. Expression, purification, crystallization and preliminary crystallographic analysis of the phosphoglycerate kinase from Acinetobacter baumannii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:790-2. [PMID: 22750866 PMCID: PMC3388923 DOI: 10.1107/s1744309112020222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/05/2012] [Indexed: 06/01/2023]
Abstract
Acinetobacter baumannii is a common multidrug-resistant clinical pathogen that is often found in hospitals. The A. baumannii phosphoglycerate kinase (AbPGK) is involved in the key energy-producing pathway of glycolysis and presents a potential target for antibiotic development. AbPGK has been expressed and purified; it was crystallized using lithium sulfate as the precipitant. The AbPGK crystals belonged to space group P222(1). They diffracted to a resolution of 2.5 Å using synchrotron radiation at the Canadian Light Source.
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Affiliation(s)
- Kayla Baretta
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig Garen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jiang Yin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Niu C, Yin J, Cherney MM, James MNG. Expression, purification and preliminary crystallographic analysis of Rv2247, the β subunit of acyl-CoA carboxylase (ACCD6) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1637-40. [PMID: 22139186 PMCID: PMC3232159 DOI: 10.1107/s1744309111038413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 09/19/2011] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) acyl-CoA carboxylase is involved in the biosynthesis of mycolic acids, which are a key component of the bacillus cell wall. The Mtb genome encodes six acyl-CoA carboxylase β subunits (ACCD1-6), three of which (ACCD4-6) are essential for survival of the pathogen on minimal medium. Mtb ACCD6 has been expressed, purified and crystallized. The two forms of Mtb ACCD6 crystals belonged to space groups P4(1)2(1)2 and P2(1)2(1)2(1) and diffracted to 2.9 and 2.5 Å resolution, respectively, at a synchrotron-radiation source.
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Affiliation(s)
- Chunying Niu
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Bateman KS, James MNG. Plant protein proteinase inhibitors: structure and mechanism of inhibition. Curr Protein Pept Sci 2011; 12:340-7. [PMID: 21418022 DOI: 10.2174/138920311796391124] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/14/2011] [Indexed: 01/04/2023]
Abstract
This review outlines known examples of the three-dimensional structures of protein proteinase inhibitors from plants. Three families of enzymes, serine proteinases, carboxypeptidases and cysteine proteinases, are targeted by at least a dozen inhibitor families, with the majority of them adopting the standard mechanism of inhibition towards the serine proteinases. All of the inhibitors discussed maintain compact and stable inhibitory domains that bind to the active site of their target proteinases and prevent access to the substrate molecules. One interesting highlight is the knottin group. Three separate inhibitor families utilize the overall knottin fold in a different way. This fold can accommodate extensive sequence variation and for each of the squash, Mirabilis and Potato carboxypeptidase families, the proteinase-binding residues are found at a different location. Plants have also evolved additional strategies to regulate proteinase activity, such as linking inhibitory domains and targeting multiple enzymes at once. The structural aspects of these strategies are discussed in the review.
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Affiliation(s)
- Katherine S Bateman
- Department of Biochemistry, School of Molecular & Systems Medicine, Faculty of Medicine & Dentistry, 431a Medical Sciences Building, University of Alberta, Edmonton T6G2H7, Canada
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Baral PK, Wieland B, Swayampakula M, Polymenidou M, Aguzzi A, Kav NNV, James MNG. Crystallization and preliminary X-ray diffraction analysis of prion protein bound to the Fab fragment of the POM1 antibody. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1211-3. [PMID: 22102029 PMCID: PMC3212364 DOI: 10.1107/s1744309111026273] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/01/2011] [Indexed: 11/10/2022]
Abstract
Prion diseases are neurodegenerative diseases that are characterized by the conversion of the cellular prion protein PrP(c) to the pathogenic isoform PrP(sc). Several antibodies are known to interact with the cellular prion protein and to inhibit this transition. An antibody Fab fragment, Fab POM1, was produced that recognizes a structural motif of the C-terminal domain of mouse prion protein. To study the mechanism by which Fab POM1 recognizes and binds the prion molecule, the complex between Fab POM1 and the C-terminal domain of mouse prion (residues 120-232) was prepared and crystallized. Crystals of this binary complex belonged to the monoclinic space group C2, with unit-cell parameters a = 83.68, b = 106.9, c = 76.25 Å, β = 95.6°.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2P6, Canada
| | - Barbara Wieland
- Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2P6, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2P6, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Magdalini Polymenidou
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0670, USA
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Nat N. V. Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Michael N. G. James
- Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2P6, Canada
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17
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Cherney MM, Cherney LT, Garen CR, James MNG. The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs. J Mol Biol 2011; 413:844-56. [PMID: 21963988 DOI: 10.1016/j.jmb.2011.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Revised: 08/31/2011] [Accepted: 09/04/2011] [Indexed: 10/17/2022]
Abstract
Phosphoribosyl pyrophosphate (PRPP) synthetase catalyzes the transfer of the pyrophosphate group from ATP to ribose-5-phosphate (R5P) yielding PRPP and AMP. PRPP is an essential metabolite that plays a central role in cellular metabolism. The enzyme from a thermophilic archaeon Thermoplasma volcanium (Tv) was expressed in Escherichia coli, crystallized, and its X-ray molecular structure was determined in a complex with its substrate R5P and with substrate analogs β,γ-methylene ATP and ADP in two monoclinic crystal forms, P2(1). The β,γ-methylene ATP- and the ADP-bound binary structures were determined from crystals grown from ammonium sulfate solutions; these crystals diffracted to 1.8 Å and 1.5 Å resolutions, respectively. Crystals of the ternary complex with ADP-Mg(2+) and R5P were grown from a polyethylene glycol solution in the absence of sulfate ions, and they diffracted to 1.8 Å resolution; the unit cell is approximately double the size of the unit cell of the crystals grown in the presence of sulfate. The Tv PRPP synthetase adopts two conformations, open and closed, at different stages in the catalytic cycle. The binding of substrates, R5P and ATP, occurs with PRPP synthetase in the open conformation, whereas catalysis presumably takes place with PRPP synthetase in the closed conformation. The Tv PRPP synthetase forms a biological dimer in contrast to the tetrameric or hexameric quaternary structures of the Methanocaldococcus jannaschii and Bacillus subtilis PRPP synthetases, respectively.
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Affiliation(s)
- Maia M Cherney
- Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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18
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Krishnaswamy S, Baral PK, James MNG, Kav NNV. Site-directed mutagenesis of histidine 69 and glutamic acid 148 alters the ribonuclease activity of pea ABR17 (PR10.4). Plant Physiol Biochem 2011; 49:958-62. [PMID: 21600779 DOI: 10.1016/j.plaphy.2010.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 10/12/2010] [Indexed: 05/21/2023]
Abstract
Pea abscisic acid responsive (ABR17) protein is a member of the pathogenesis-related 10 (PR10) family of proteins and its ribonuclease (RNase) activity has been reported previously. In order to investigate the amino acids important for the demonstrated ribonuclease activity of ABR17, site-directed mutants H69L and E148A were generated, expressed in Escherichia coli and purified to homogeneity. These mutations affected RNase activity differently; the H69L mutant exhibited a decreased RNase activity whereas E148A exhibited an elevated activity. A structural model for pea ABR17 has been generated using the three dimensional structure of Lupinus luteus PR10 protein in order to explain the possible effects of the H69L and the E148A mutations on substrate binding and catalysis.
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Affiliation(s)
- Sowmya Krishnaswamy
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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19
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Yin J, Garen CR, Bateman K, Yu M, Alipio Lyon EZ, Habel J, Kim H, Hung LW, Kim CY, James MNG. Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:959-63. [PMID: 21821905 PMCID: PMC3151138 DOI: 10.1107/s1744309111017611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/10/2011] [Indexed: 11/11/2022]
Abstract
The gene product of the open reading frame Rv3340 from Mycobacterium tuberculosis is annotated as encoding a probable O-acetylhomoserine (OAH) sulfhydrylase (MetC), an enzyme that catalyzes the last step in the biosynthesis of methionine, which is an essential amino acid in bacteria and plants. Following overexpression in Escherichia coli, the M. tuberculosis MetC enzyme was purified and crystallized using the hanging-drop vapor-diffusion method. Native diffraction data were collected from crystals belonging to space group P2(1) and were processed to a resolution of 2.1 Å.
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Affiliation(s)
- Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Katherine Bateman
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Minmin Yu
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Emily Z. Alipio Lyon
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeff Habel
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Heungbok Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Li-wei Hung
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Chang-Yub Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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20
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Yin J, Garen G, Garen C, James MNG. Expression, purification and preliminary crystallographic analysis of Rv3002c, the regulatory subunit of acetolactate synthase (IlvH) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:933-6. [PMID: 21821899 DOI: 10.1107/s1744309111021105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/01/2011] [Indexed: 11/10/2022]
Abstract
Branched amino-acid biosynthesis is important to bacterial pathogens such as Mycobacterium tuberculosis (Mtb), a microorganism that presently causes more deaths in humans than any other prokaryotic pathogen (http://www.who.int/tb). In this study, the molecular cloning, expression, purification, crystallization and preliminary crystallographic analysis of recombinant IlvH, the small regulatory subunit of acetohydroxylic acid synthase (AHAS) in Mtb, are reported. AHAS carries out the first common reaction in the biosynthesis of valine, leucine and isoleucine. AHAS is an essential enzyme in Mtb and its inactivation leads to a lethal phenotype [Sassetti et al. (2001), Proc. Natl Acad. Sci. USA, 98, 12712-12717]. Thus, inhibitors of AHAS could potentially be developed into novel anti-Mtb therapies.
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Affiliation(s)
- Jiang Yin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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21
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Watanabe N, James MNG. Structural insights for the substrate recognition mechanism of LL-diaminopimelate aminotransferase. Biochim Biophys Acta 2011; 1814:1528-33. [PMID: 21435399 DOI: 10.1016/j.bbapap.2011.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 03/02/2011] [Accepted: 03/09/2011] [Indexed: 11/25/2022]
Abstract
The enzymes involved in the lysine biosynthetic pathway have long been considered to be attractive targets for novel antibiotics due to the absence of this pathway in humans. Recently, a novel pyridoxal 5'-phosphate (PLP) dependent enzyme called LL-diaminopimelate aminotransferase (LL-DAP-AT) was identified in the lysine biosynthetic pathway of plants and Chlamydiae. Understanding its function and substrate recognition mechanism would be an important initial step toward designing novel antibiotics targeting LL-DAP-AT. The crystal structures of LL-DAP-AT from Arabidopsis thaliana in complex with various substrates and analogues have been solved recently. These structures revealed how L-glutamate and LL-DAP are recognized by LL-DAP-AT without significant conformational changes in the enzyme's backbone structure. This review article summarizes the recent developments in the structural characterization and the inhibitor design of LL-DAP-AT from A. thaliana. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.
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Affiliation(s)
- Nobuhiko Watanabe
- Department of Biochemistry, School of Medicine and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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22
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Bateman KS, Cherney MM, Mahuran DJ, Tropak M, James MNG. Crystal structure of β-hexosaminidase B in complex with pyrimethamine, a potential pharmacological chaperone. J Med Chem 2011; 54:1421-9. [PMID: 21265544 DOI: 10.1021/jm101443u] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
β-Hexosaminidases (β-hex) are a group of glycosyl hydrolase isozymes that break down neutral and sialylated glycosphingolipids in the lysosomes, thereby preventing their buildup in neuronal cells. Some mutants of β-hex have decreased folding stability that results in adult-onset forms of lysosomal storage diseases. However, prevention of the harmful accumulation of glycolipids only requires 10% of wild-type activity. Pyrimethamine (PYR) is a potential pharmacological chaperone that works by stabilizing these mutant enzymes sufficiently to allow more β-hex to arrive in the lysosome, where it can carry out its function. An X-ray structure of the complex between human β-hexosaminidase B (HexB) and PYR has been determined to 2.8 Å. PYR binds to the active site of HexB where several favorable van der Waals contacts and hydrogen bonds are introduced. Small adjustments of the enzyme structure are required to accommodate the ligand, and details of the inhibition and stabilization properties of PYR are discussed.
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Affiliation(s)
- Katherine S Bateman
- Department of Biochemistry, 4-29 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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23
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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24
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Cherney MM, Lecaille F, Kienitz M, Nallaseth FS, Li Z, James MNG, Brömme D. Structure-activity analysis of cathepsin K/chondroitin 4-sulfate interactions. J Biol Chem 2010; 286:8988-98. [PMID: 21193413 DOI: 10.1074/jbc.m110.126706] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the presence of oligomeric chondroitin 4-sulfate (C4-S), cathepsin K (catK) forms a specific complex that was shown to be the source of the major collagenolytic activity in bone osteoclasts. C4-S forms multiple contacts with amino acid residues on the backside of the catK molecule that help to facilitate complex formation. As cathepsin L does not exhibit a significant collagenase activity in the presence or in the absence of C4-S, we substituted the C4-S interacting residues in catK with those of cathepsin L. Variants revealed altered collagenolytic activities with the largest inhibitory effect shown by the hexavariant M5. None of the variants showed a reduction in their gelatinolytic and peptidolytic activities when compared with wild-type catK, indicating no structural alteration within their active sites. However, the crystal structure of the M5 variant in the presence of oligomeric C4-S revealed a different binding of chondroitin 4-sulfate. C4-S is not continuously ordered as it is in the wild-type catK·C4-S complex. The orientation and the direction of the hexasaccharide on the catK surface have changed, so that the hexasaccharide is positioned between two symmetry-related molecules. Only one M5 variant molecule of the dimer that is present in the asymmetric unit interacts with C4-S. These substitutions have changed the mode of catK binding to C4-S and, as a result, have likely affected the collagenolytic potential of the variant. The data presented here support our hypothesis that distinct catK/C4-S interactions are necessary for the collagenolytic activity of the enzyme.
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Affiliation(s)
- Maia M Cherney
- Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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25
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Kondo MY, Okamoto DN, Santos JAN, Juliano MA, Oda K, Pillai B, James MNG, Juliano L, Gouvea IE. Studies on the catalytic mechanism of a glutamic peptidase. J Biol Chem 2010; 285:21437-45. [PMID: 20442413 DOI: 10.1074/jbc.m110.122432] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Scytalidoglutamic peptidase (SGP) is the prototype of fungal glutamic peptidases that are characteristically pepstatin insensitive. These enzymes have a unique catalytic dyad comprised of Gln(53) and Glu(136) that activate a bound water molecule for nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. The hydrolysis by SGP at peptide bonds with proline in the P(1)' position is a rare event among peptidases that we investigated using the series of fluorescence resonance energy transfer peptides, Abz-KLXPSKQ-EDDnp, compared with the series Abz-KLXSSKQ-EDDnp. The preference observed in these two series for Phe and His over Leu, Ile, Val, Arg, and Lys, seems to be related to the structure of the S(1) subsite of SGP. These results and the pH profiles of SGP activity showed that its S(1) subsite can accommodate the benzyl group of Phe at pH 4 as well as the positively charged imidazolium group of His. In the pH range 2 to 7, SGP maintains its structure and activity, but at pH 8 or higher it is irreversibly denatured. The intrinsic fluorescence of the Trp residues of SGP were sensitive to the titration of carboxyl groups having low pK values; this can be attributed to the buried Asp(57) and/or Asp(43) as described in SGP three-dimensional structure. The solvent kinetic isotope effects and the proton inventory experiments support a mechanism for the glutamic peptidase SGP that involves the nucleophilic attack of the general base (Glu(136)) activated water, and establish a fundamental role of the S(1) subsite interactions in promoting catalysis.
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Affiliation(s)
- Márcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
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26
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Sankaranarayanan R, Cherney MM, Garen C, Garen G, Niu C, Yuan M, James MNG. The molecular structure of ornithine acetyltransferase from Mycobacterium tuberculosis bound to ornithine, a competitive inhibitor. J Mol Biol 2010; 397:979-90. [PMID: 20184895 DOI: 10.1016/j.jmb.2010.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/05/2010] [Accepted: 02/10/2010] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis ornithine acetyltransferase (Mtb OAT; E.C. 2.3.1.35) is a key enzyme of the acetyl recycling pathway during arginine biosynthesis. It reversibly catalyzes the transfer of the acetyl group from N-acetylornithine (NAORN) to L-glutamate. Mtb OAT is a member of the N-terminal nucleophile fold family of enzymes. The crystal structures of Mtb OAT in native form and in its complex with ornithine (ORN) have been determined at 1.7 and 2.4 A resolutions, respectively. ORN is a competitive inhibitor of this enzyme against L-glutamate as substrate. Although the acyl-enzyme complex of Streptomyces clavuligerus ornithine acetyltransferase has been determined, ours is the first crystal structure to be reported of an ornithine acetyltransferase in complex with an inhibitor. ORN binding does not alter the structure of Mtb OAT globally. However, its presence stabilizes the three C-terminal residues that are disordered and not observed in the native structure. Also, stabilization of the C-terminal residues by ORN reduces the size of the active-site pocket volume in the structure of the ORN complex. The interactions of ORN and the protein residues of Mtb OAT unambiguously delineate the active-site residues of this enzyme in Mtb. Moreover, modeling studies carried out with NAORN based on the structure of the ORN-Mtb OAT complex reveal important interactions of the carbonyl oxygen of the acetyl group of NAORN with the main-chain nitrogen atom of Gly128 and with the side-chain oxygen of Thr127. These interactions likely help in the stabilization of oxyanion formation during enzymatic reaction and also will polarize the carbonyl carbon-oxygen bond, thereby enabling the side-chain atom O(gamma 1) of Thr200 to launch a nucleophilic attack on the carbonyl-carbon atom of the acetyl group of NAORN.
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Affiliation(s)
- Ramasamy Sankaranarayanan
- Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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27
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Zhang Y, Cherney MM, Solomonson M, Liu J, James MNG, Weiner JH. Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:839-42. [PMID: 19652354 PMCID: PMC2720348 DOI: 10.1107/s1744309109027535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/07/2009] [Indexed: 03/19/2023]
Abstract
The gene product of open reading frame AFE_1293 from Acidithiobacillus ferrooxidans ATCC 23270 is annotated as encoding a sulfide:quinone oxidoreductase, an enzyme that catalyses electron transfer from sulfide to quinone. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. The native crystals belonged to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 131.7, c = 208.8 A, and diffracted to 2.3 A resolution. Preliminary crystallographic analysis indicated the presence of a dimer in the asymmetric unit, with an extreme value of the Matthews coefficient (V(M)) of 4.53 A(3) Da(-1) and a solvent content of 72.9%.
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Affiliation(s)
- Yanfei Zhang
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan 410083, People’s Republic of China
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Matthew Solomonson
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jianshe Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan 410083, People’s Republic of China
| | - Michael N. G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joel H. Weiner
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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28
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Cherney LT, Cherney MM, Garen CR, James MNG. The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine. J Mol Biol 2009; 388:85-97. [PMID: 19265706 DOI: 10.1016/j.jmb.2009.02.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 02/17/2009] [Accepted: 02/20/2009] [Indexed: 10/21/2022]
Abstract
The biosynthesis of arginine is an essential function for the metabolism of Mycobacterium tuberculosis (Mtb) and for the metabolism of many other microorganisms. The arginine repressor (ArgR) proteins control the transcription of genes encoding the arginine biosynthetic enzymes; they belong to repressors having one of the most intricate oligomerization patterns. Here, we present the crystal structure of the MtbArgR hexamer bound to three copies of the 20 base-pair DNA operator and to the co-repressor, L-arginine, determined to 3.3 A resolution. This is the first ternary structure of an intact hexameric ArgR in complex with its DNA operator. The structure reported here is very different from the suggested models of the ternary ArgR-DNA complexes; it has revealed the sophisticated symmetry of the complex and the presence of two remarkably different protomer conformations, folded and extended. Both features provide flexibility to DNA binding and are important for understanding the detailed function of ArgRs. Two of the 20 base-pair DNA operators align in a unified double-helical structure, suggesting the possible presence of a double ARG box in the promoter region of the Mtb arginine operon. Two pairs of protomers bind to the unified double ARG box so that the two folded protomers bind to the central half-sites of the double ARG box, whereas the two extended protomers bind to the remote half-sites. The protomers of the third pair bound to the single DNA operator also have a folded and an extended conformation. A probable mechanism for arginine repression is suggested on the basis of this structure.
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Affiliation(s)
- Leonid T Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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29
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Cherney LT, Cherney MM, Garen CR, Lu GJ, James MNG. Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis. J Mol Biol 2008; 384:1330-40. [PMID: 18952097 DOI: 10.1016/j.jmb.2008.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 10/02/2008] [Accepted: 10/03/2008] [Indexed: 11/25/2022]
Abstract
The arginine repressor (ArgR) from Mycobacterium tuberculosis (Mtb) is a gene product encoded by the open reading frame Rv1657. It regulates the L-arginine concentration in cells by interacting with ARG boxes in the promoter regions of the arginine biosynthesis and catabolism operons. Here we present a 2.5-A structure of MtbArgR in complex with a 16-bp DNA operator in the absence of arginine. A biological trimer of the protein-DNA complex is formed via the crystallographic 3-fold symmetry axis. The N-terminal domain of MtbArgR has a winged helix-turn-helix motif that binds to the major groove of the DNA. This structure shows that, in the absence of arginine, the ArgR trimer can bind three ARG box half-sites. It also reveals the structure of the whole MtbArgR molecule itself containing both N-terminal and C-terminal domains.
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Affiliation(s)
- Leonid T Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, 431 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
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Biswal BK, Morisseau C, Garen G, Cherney MM, Garen C, Niu C, Hammock BD, James MNG. The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor. J Mol Biol 2008; 381:897-912. [PMID: 18585390 PMCID: PMC2866126 DOI: 10.1016/j.jmb.2008.06.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 06/09/2008] [Accepted: 06/10/2008] [Indexed: 11/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as well as in the processing of signaling molecules. Herein, we report the crystal structures of unbound Mtb EHB and Mtb EHB bound to a potent, low-nanomolar (IC(50) approximately 19 nM) urea-based inhibitor at 2.1 and 2.4 A resolution, respectively. The enzyme is a homodimer; each monomer adopts the classical alpha/beta hydrolase fold that composes the catalytic domain; there is a cap domain that regulates access to the active site. The catalytic triad, comprising Asp104, His333 and Asp302, protrudes from the catalytic domain into the substrate binding cavity between the two domains. The urea portion of the inhibitor is bound in the catalytic cavity, mimicking, in part, the substrate binding; the two urea nitrogen atoms donate hydrogen bonds to the nucleophilic carboxylate of Asp104, and the carbonyl oxygen of the urea moiety receives hydrogen bonds from the phenolic oxygen atoms of Tyr164 and Tyr272. The phenolic oxygen groups of these two residues provide electrophilic assistance during the epoxide hydrolytic cleavage. Upon inhibitor binding, the binding-site residues undergo subtle structural rearrangement. In particular, the side chain of Ile137 exhibits a rotation of around 120 degrees about its C(alpha)-C(beta) bond in order to accommodate the inhibitor. These findings have not only shed light on the enzyme mechanism but also have opened a path for the development of potent inhibitors with good pharmacokinetic profiles against all Mtb EHs of the alpha/beta type.
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Affiliation(s)
- Bichitra K. Biswal
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
| | - Christophe Morisseau
- Department of Entomology and UCD Cancer Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Grace Garen
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
| | - Craig Garen
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
| | - Chunying Niu
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
| | - Bruce D. Hammock
- Department of Entomology and UCD Cancer Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Michael N. G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Canada T6G2H7
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31
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Yin J, Garen CR, Cherney MM, Cherney LT, James MNG. Expression, purification and preliminary crystallographic analysis of N-acetylglucosamine-1-phosphate uridylyltransferase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:805-8. [PMID: 18765909 PMCID: PMC2531282 DOI: 10.1107/s1744309108024500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Accepted: 07/31/2008] [Indexed: 05/26/2023]
Abstract
The gene product of open reading frame Rv1018c from Mycobacterium tuberculosis is annotated as encoding a probable N-acetylglucosamine 1-phosphate uridylyltransferase (MtbGlmU), an enzyme that catalyzes the biosynthesis of UDP-N-acetylglucosamine, a precursor common to lipopolysaccharide and peptidoglycan biosynthesis. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. Native diffraction data were collected from crystals belonging to space group R32 and processed to a resolution of 2.2 A.
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Affiliation(s)
- Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leonid T. Cherney
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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32
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Cherney LT, Cherney MM, Garen CR, Lu GJ, James MNG. Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr 2008; 64:950-6. [PMID: 18703843 PMCID: PMC2631108 DOI: 10.1107/s0907444908021513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 07/11/2008] [Indexed: 11/11/2022]
Abstract
The Mycobacterium tuberculosis (Mtb) gene product encoded by open reading frame Rv1657 is an arginine repressor (ArgR). All genes involved in the L-arginine (hereafter arginine) biosynthetic pathway are essential for optimal growth of the Mtb pathogen, thus making MtbArgR a potential target for drug design. The C-terminal domains of arginine repressors (CArgR) participate in oligomerization and arginine binding. Several crystal forms of CArgR from Mtb (MtbCArgR) have been obtained. The X-ray crystal structures of MtbCArgR were determined at 1.85 A resolution with bound arginine and at 2.15 A resolution in the unliganded form. These structures show that six molecules of MtbCArgR are arranged into a hexamer having approximate 32 point symmetry that is formed from two trimers. The trimers rotate relative to each other by about 11 degrees upon binding arginine. All residues in MtbCArgR deemed to be important for hexamer formation and for arginine binding have been identified from the experimentally determined structures presented. The hexamer contains six regular sites in which the arginine molecules have one common binding mode and three sites in which the arginine molecules have two overlapping binding modes. The latter sites only bind the ligand at high (200 mM) arginine concentrations.
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Affiliation(s)
- Leonid T. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - George J. Lu
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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33
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Li Z, Kienetz M, Cherney MM, James MNG, Brömme D. The crystal and molecular structures of a cathepsin K:chondroitin sulfate complex. J Mol Biol 2008; 383:78-91. [PMID: 18692071 DOI: 10.1016/j.jmb.2008.07.038] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/10/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
Abstract
Cathepsin K is the major collagenolytic enzyme produced by bone-resorbing osteoclasts. We showed earlier that the unique triple-helical collagen-degrading activity of cathepsin K depends on the formation of complexes with bone-or cartilage-resident glycosaminoglycans, such as chondroitin 4-sulfate (C4-S). Here, we describe the crystal structure of a 1:n complex of cathepsin K:C4-S inhibited by E64 at a resolution of 1.8 A. The overall structure reveals an unusual "beads-on-a-string"-like organization. Multiple cathepsin K molecules bind specifically to a single cosine curve-shaped strand of C4-S with each cathepsin K molecule interacting with three disaccharide residues of C4-S. One of the more important sets of interactions comes from a single turn of helix close to the N terminus of the proteinase containing a basic amino acid triplet (Arg8-Lys9-Lys10) that forms multiple hydrogen bonds either to the caboxylate or to the 4-sulfate groups of C4-S. Altogether, the binding sites with C4-S are located in the R-domain of cathepsin K and are distant from its active site. This explains why the general proteolytic activity of cathepsin K is not affected by the binding of chondroitin sulfate. Biochemical analyses of cathepsin K and C4-S mixtures support the presence of a 1:n complex in solution; a dissociation constant, K(d), of about 10 nM was determined for the interaction between cathepsin K and C4-S.
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Affiliation(s)
- Zhenqiang Li
- Mount Sinai School of Medicine, Department of Human Genetics, New York, NY 10029, USA
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Witholt SJ, Sankaranarayanan R, Garen CR, Cherney MM, Cherney LT, James MNG. Expression, purification, crystallization and preliminary X-ray analysis of Rv3117, a probable thiosulfate sulfurtransferase (CysA3) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:541-4. [PMID: 18540071 PMCID: PMC2496863 DOI: 10.1107/s1744309108014449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 05/13/2008] [Indexed: 05/26/2023]
Abstract
The gene product of open reading frame Rv3117 from Mycobacterium tuberculosis (Mtb) strain H37Rv is annotated as encoding a probable rhodanese-like thiosulfate sulfurtransferase (MtbCysA3). MtbCysA3 was expressed and purified and then crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected and processed to a maximum resolution of 2.5 A. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 38.86, b = 91.43, c = 83.57 A, beta = 96.6 degrees . Preliminary diffraction data shows that two molecules are present in the asymmetric unit; this corresponds to a V(M) of 2.4 A(3) Da(-1).
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Affiliation(s)
- Sarah J. Witholt
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ramasamy Sankaranarayanan
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leonid T. Cherney
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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35
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Huitema C, Zhang J, Yin J, James MNG, Vederas JC, Eltis LD. Heteroaromatic ester inhibitors of hepatitis A virus 3C proteinase: Evaluation of mode of action. Bioorg Med Chem 2008; 16:5761-77. [PMID: 18407505 PMCID: PMC7125897 DOI: 10.1016/j.bmc.2008.03.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/24/2008] [Indexed: 11/23/2022]
Abstract
The related 3C and 3C-like proteinase (3C(pro) and 3CL(pro)) of picornaviruses and coronaviruses, respectively, are good drug targets. As part of an effort to generate broad-spectrum inhibitors of these enzymes, we screened a library of inhibitors based on a halopyridinyl ester from a previous study of the severe acute respiratory syndrome (SARS) 3CL proteinase against Hepatitis A virus (HAV) 3C(pro). Three of the compounds, which also had furan rings, inhibited the cleavage activity of HAV 3C(pro) with K(ic)s of 120-240nM. HPLC-based assays revealed that the inhibitors were slowly hydrolyzed by both HAV 3C(pro) and SARS 3CL(pro), confirming the identity of the expected products. Mass spectrometric analyses indicated that this hydrolysis proceeded via an acyl-enzyme intermediate. Modeling studies indicated that the halopyridinyl moiety of the inhibitor fits tightly into the S1-binding pocket, consistent with the lack of tolerance of the inhibitors to modification in this portion of the molecule. These compounds are among the most potent non-peptidic inhibitors reported to date against a 3C(pro).
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Affiliation(s)
- Carly Huitema
- Department of Microbiology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia, Canada V6T 1Z3
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36
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Zhang J, Huitema C, Niu C, Yin J, James MNG, Eltis LD, Vederas JC. Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase. Bioorg Chem 2008; 36:229-40. [PMID: 18295820 PMCID: PMC7112044 DOI: 10.1016/j.bioorg.2008.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 12/29/2007] [Accepted: 01/03/2008] [Indexed: 12/30/2022]
Abstract
The severe acute respiratory syndrome (SARS) virus depends on a chymotrypsin-like cysteine proteinase (3CL(pro)) to process the translated polyproteins to functional viral proteins. This enzyme is a target for the design of potential anti-SARS drugs. A series of ketones and corresponding mono- and di-fluoro ketones having two or three aromatic rings were synthesized as possible reversible inhibitors of SARS 3CL(pro). The design was based on previously established potent inhibition of the enzyme by oxa analogues (esters), which also act as substrates. Structure-activity relationships and modeling studies indicate that three aromatic rings, including a 5-bromopyridin-3-yl moiety, are key features for good inhibition of SARS 3CL(pro). Compound 11d, 2-(5-bromopyridin-3-yl)-1-(5-(4-chlorophenyl)furan-2-yl)ethanone and its alpha-monofluorinated analogue 12d, gave the best reversible inhibition with IC(50) values of 13 mircoM and 28 microM, respectively. In contrast to inhibitors having two aromatic rings, alpha-fluorination of compounds with three rings unexpectedly decreased the inhibitory activity.
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Affiliation(s)
- Jianmin Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
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37
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Lee TW, James MNG. 1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB). Biochim Biophys Acta 2007; 1784:319-34. [PMID: 18157955 DOI: 10.1016/j.bbapap.2007.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 11/13/2007] [Accepted: 11/15/2007] [Indexed: 11/29/2022]
Abstract
Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs. The densities at pH 4.2 were assigned as a tetrapeptide, Asp-Ala-Ile-Tyr, whereas those at pH 7.3 were assigned as a tyrosine molecule and a leucine molecule existing at equal occupancies in both of the SGPB molecules in the asymmetric unit. Refinement with relaxed geometric restraints resulted in molecular structures representing mixtures of the second tetrahedral intermediates and the enzyme-product complexes of SGPB existing in a pH-dependent equilibrium. Structural comparisons with the complexes of SGPB with turkey ovomucoid third domain (OMTKY3) and its variants have shown that, upon the formation of the tetrahedral intermediate, residues Glu192A to Gly193 of SGPB move towards the alpha-carboxylate O of residue P1 of the bound species, and adjustments in the side-chain conformational angles of His57 and Ser195 of SGPB favor the progression of the catalytic mechanism of SGPB.
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Affiliation(s)
- Ting-Wai Lee
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Room 4-29, Medical Sciences Building, Edmonton, Alberta T6G 2H7, Canada
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38
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Sankaranarayanan R, Cherney MM, Cherney LT, Garen CR, Moradian F, James MNG. The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism. J Mol Biol 2007; 375:1052-63. [PMID: 18062991 DOI: 10.1016/j.jmb.2007.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/06/2007] [Accepted: 11/09/2007] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis ornithine carbamoyltransferase (Mtb OTC) catalyzes the sixth step in arginine biosynthesis; it produces citrulline from carbamoyl phosphate (CP) and ornithine (ORN). Here, we report the crystal structures of Mtb OTC in orthorhombic (form I) and hexagonal (form II) space groups. The molecules in form II are complexed with CP and l-norvaline (NVA); the latter is a competitive inhibitor of OTC. The asymmetric unit in form I contains a pseudo hexamer with 32 point group symmetry. The CP and NVA in form II induce a remarkable conformational change in the 80s and the 240s loops with the displacement of these loops towards the active site. The displacement of these loops is strikingly different from that seen in other OTC structures. In addition, the ligands induce a domain closure of 4.4 degrees in form II. Sequence comparison of active-site residues of Mtb OTC with several other OTCs of known structure reveals that they are virtually identical. The interactions involving the active-site residues of Mtb OTC with CP and NVA and a modeling study of ORN in the form II structure strongly rule out an earlier proposed mechanistic role of Cys264 in catalysis and suggest a possible mechanism for OTC. Our results strongly support the view that ORN with an already deprotonated N(epsilon) atom is the species that binds to the enzyme and that one of the phosphate oxygen atoms of CP is likely to be involved in accepting a proton from the doubly protonated N(epsilon) atom of ORN. We have interpreted this deprotonation as part of the collapse of the transition state of the reaction.
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Affiliation(s)
- Ramasamy Sankaranarayanan
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Lu GJ, Garen CR, Cherney MM, Cherney LT, Lee C, James MNG. Expression, purification and preliminary X-ray analysis of the C-terminal domain of an arginine repressor protein from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:936-9. [PMID: 18007044 PMCID: PMC2339742 DOI: 10.1107/s1744309107046374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 09/20/2007] [Indexed: 11/11/2022]
Abstract
The gene product of an open reading frame Rv1657 from Mycobacterium tuberculosis is a putative arginine repressor protein (ArgR), a transcriptional factor that regulates the expression of arginine-biosynthetic enzymes. Rv1657 was expressed and purified and a C-terminal domain was crystallized using the hanging-drop vapour-diffusion method. Diffraction data were collected and processed to a resolution of 2.15 A. The crystals belong to space group P1 and the Matthews coefficient suggests that the crystals contain six C-terminal domain molecules per unit cell. Previous structural and biochemical studies on the arginine repressor proteins from other organisms have likewise shown the presence of six molecules per unit cell.
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Affiliation(s)
- George J. Lu
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leonid T. Cherney
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Cecilia Lee
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, The University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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40
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Niu C, Yin J, Zhang J, Vederas JC, James MNG. Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro. Bioorg Med Chem 2007; 16:293-302. [PMID: 17931870 PMCID: PMC7127602 DOI: 10.1016/j.bmc.2007.09.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 09/17/2007] [Accepted: 09/19/2007] [Indexed: 11/05/2022]
Abstract
The 3C-like main proteinase of the severe acute respiratory syndrome (SARS) coronavirus, SARS-CoV Mpro, is widely considered to be a major drug target for the development of anti-SARS treatment. Based on the chemical structure of a lead compound from a previous screening, we have designed and synthesized a number of non-peptidyl inhibitors, some of which have shown significantly improved inhibitory activity against SARS-CoV Mpro with IC50 values of ∼60 nM. In the absence of SARS-CoV Mpro crystal structures in complex with these synthetic inhibitors, molecular docking tools have been employed to study possible interactions between these inhibitors and SARS-CoV Mpro. The docking results suggest two major modes for the initial binding of these inhibitors to the active site of SARS-CoV Mpro. They also establish a structural basis for the ‘core design’ of these inhibitors by showing that the 3-chloropyridine functions common to all of the present inhibitors tend to cluster in the S1 specificity pocket. In addition, intrinsic flexibility in the S4 pocket allows for the accommodation of bulky groups such as benzene rings, suggesting that this structural plasticity can be further exploited for optimizing inhibitor–enzyme interactions that should promote a tighter binding mode. Most importantly, our results provide the structural basis for rational design of wide-spectrum antiviral drugs targeting the chymotrypsin-like cysteine proteinases from coronaviruses and picornaviruses.
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Affiliation(s)
- Chunying Niu
- Group in Protein Structure and Function, 431 Medical Science Building, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
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41
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Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MNG. Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. Biochem Biophys Res Commun 2007; 363:547-53. [PMID: 17889830 DOI: 10.1016/j.bbrc.2007.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 09/04/2007] [Indexed: 10/22/2022]
Abstract
Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3A and 2.2A resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.
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Affiliation(s)
- Bindu Pillai
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta, Canada T6G 2H7
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42
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Watanabe N, Cherney MM, van Belkum MJ, Marcus SL, Flegel MD, Clay MD, Deyholos MK, Vederas JC, James MNG. Crystal Structure of ll-Diaminopimelate Aminotransferase from Arabidopsis thaliana: A Recently Discovered Enzyme in the Biosynthesis of l-Lysine by Plants and Chlamydia. J Mol Biol 2007; 371:685-702. [PMID: 17583737 DOI: 10.1016/j.jmb.2007.05.061] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 05/21/2007] [Accepted: 05/22/2007] [Indexed: 11/18/2022]
Abstract
The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism.
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Affiliation(s)
- Nobuhiko Watanabe
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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43
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Murillo AC, Li HY, Alber T, Baker EN, Berger JM, Cherney LT, Cherney MM, Cho YS, Eisenberg D, Garen CR, Goulding CW, Hung LW, Ioerger TR, Jacobs WR, James MNG, Kim C, Krieger I, Lott JS, Sankaranarayanan R, Segelke BW, Terwilliger TC, Wang F, Wang S, Sacchettini JC. High throughput crystallography of TB drug targets. Infect Disord Drug Targets 2007; 7:127-139. [PMID: 17970224 DOI: 10.2174/187152607781001853] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Tuberculosis (TB) infects one-third of the world population. Despite 50 years of available drug treatments, TB continues to increase at a significant rate. The failure to control TB stems in part from the expense of delivering treatment to infected individuals and from complex treatment regimens. Incomplete treatment has fueled the emergence of multi-drug resistant (MDR) strains of Mycobacterium tuberculosis (Mtb). Reducing non-compliance by reducing the duration of chemotherapy will have a great impact on TB control. The development of new drugs that either kill persisting organisms, inhibit bacilli from entering the persistent phase, or convert the persistent bacilli into actively growing cells susceptible to our current drugs will have a positive effect. We are taking a multidisciplinary approach that will identify and characterize new drug targets that are essential for persistent Mtb. Targets are exposed to a battery of analyses including microarray experiments, bioinformatics, and genetic techniques to prioritize potential drug targets from Mtb for structural analysis. Our core structural genomics pipeline works with the individual laboratories to produce diffraction quality crystals of targeted proteins, and structural analysis will be completed by the individual laboratories. We also have capabilities for functional analysis and the virtual ligand screening to identify novel inhibitors for target validation. Our overarching goals are to increase the knowledge of Mtb pathogenesis using the TB research community to drive structural genomics, particularly related to persistence, develop a central repository for TB research reagents, and discover chemical inhibitors of drug targets for future development of lead compounds.
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Affiliation(s)
- A C Murillo
- Texas A&M University, Department of Biochemistry and Biophysics, College Station 77843-2128, USA
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44
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Zhang J, Pettersson HI, Huitema C, Niu C, Yin J, James MNG, Eltis LD, Vederas JC. Design, synthesis, and evaluation of inhibitors for severe acute respiratory syndrome 3C-like protease based on phthalhydrazide ketones or heteroaromatic esters. J Med Chem 2007; 50:1850-64. [PMID: 17381079 DOI: 10.1021/jm061425k] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 3C-like protease (3CLpro), which controls the severe acute respiratory syndrome (SARS) coronavirus replication, has been identified as a potential target for drug design in the treatment of SARS. A series of tetrapeptide phthalhydrazide ketones, pyridinyl esters, and their analogs have been designed, synthesized, and evaluated as potential SARS 3CLpro inhibitors. Some pyridinyl esters are identified as very potent inhibitors, with IC50 values in the nanomolar range (50-65 nM). Electrospray mass spectrometry indicates a mechanism involving acylation of the active site cysteine thiol for this class of inhibitors.
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Affiliation(s)
- Jianmin Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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45
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Lee TW, Qasim MA, Laskowski M, James MNG. Structural Insights into the Non-additivity Effects in the Sequence-to-Reactivity Algorithm for Serine Peptidases and their Inhibitors. J Mol Biol 2007; 367:527-46. [PMID: 17266986 DOI: 10.1016/j.jmb.2007.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 12/24/2006] [Accepted: 01/03/2007] [Indexed: 11/17/2022]
Abstract
Sequence-to-reactivity algorithms (SRAs) for proteins have the potential of being broadly applied in molecular design. Recently, Laskowski et al. have reported an additivity-based SRA that accurately predicts most of the standard free energy changes of association for variants of turkey ovomucoid third domain (OMTKY3) with six serine peptidases, one of which is streptogrisin B (commonly known as Streptomyces griseus peptidase B, SGPB). Non-additivity effects for residues 18I and 32I, and for residues 20I and 32I of OMTKY3 occurred when the associations with SGPB were predicted using the SRA. To elucidate precisely the mechanics of these non-additivity effects in structural terms, we have determined the crystal structures of the unbound OMTKY3 (with Gly32I as in the wild-type amino acid sequence) at a resolution of 1.16 A, the unbound Ala32I variant of OMTKY3 at a resolution of 1.23 A, and the SGPB:OMTKY3-Ala32I complex (equilibrium association constant K(a)=7.1x10(9) M(-1) at 21(+/-2) C degrees, pH 8.3) at a resolution of 1.70 A. Extensive comparisons with the crystal structure of the unbound OMTKY3 confirm our understanding of some previously addressed non-additivity effects. Unexpectedly, SGPB and OMTKY3-Ala32I form a 1:2 complex in the crystal. Comparison with the SGPB:OMTKY3 complex shows a conformational change in the SGPB:OMTKY3-Ala32I complex, resulting from a hinged rigid-body rotation of the inhibitor caused by the steric hindrance between the methyl group of Ala32IA of the inhibitor and Pro192BE of the peptidase. This perturbs the interactions among residues 18I, 20I, 32I and 36I of the inhibitor, probably resulting in the above non-additivity effects. This conformational change also introduces residue 10I as an additional hyper-variable contact residue to the SRA.
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Affiliation(s)
- Ting-Wai Lee
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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46
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Cherney LT, Cherney MM, Garen CR, Niu C, Moradian F, James MNG. Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase from Mycobacterium tuberculosis in complex with NADP(+). J Mol Biol 2007; 367:1357-69. [PMID: 17316682 DOI: 10.1016/j.jmb.2007.01.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 01/09/2007] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
The enzyme N-acetyl-gamma-glutamyl-phosphate reductase (AGPR) catalyzes the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductive dephosphorylation of N-acetyl-gamma-glutamyl-phosphate to N-acetylglutamate-gamma-semialdehyde. This reaction is part of the arginine biosynthetic pathway that is essential for some microorganisms and plants, in particular, for Mycobacterium tuberculosis (Mtb). The structures of apo MtbAGPR in the space groups P2(1)2(1)2(1) and C2 and the structure of MtbAGPR bound to the cofactor NADP(+) have been solved and analyzed. Each MtbAGPR subunit consists of alpha/beta and alpha+beta domains; NADP(+) is bound in the cleft between them. The hydrogen bonds and hydrophobic contacts between the enzyme and cofactor have been examined. Comparison of the apo and the bound enzyme structures has revealed a conformational change in MtbAGPR upon NADP(+) binding. Namely, a loop (Leu88 to His92) moves more than 5 A to confine sterically the cofactor's adenine moiety in a hydrophobic pocket. To identify the catalytically important residues in MtbAGPR, a docking of the substrate to the enzyme has been performed using the present structure of the MtbAGPR/NADP(+) complex. It reveals that residues His217 and His219 could form hydrogen bonds with the docked substrate. In addition, an ion pair could form between the substrate phosphate group and the guanidinium group of Arg114. These interactions optimally place and orient the substrate for subsequent nucleophilic attack by Cys158 on the substrate gamma-carboxyl group. His219 is the most probable general base to accept a proton from Cys158 and an adjacent ion pair interaction with the side-chain carboxyl group of Glu222 could help to stabilize the resulting positive charge on His219. For this catalytic triad to function efficiently it requires a small conformational change of the order of 1 A in the loop containing His217 and His219; this could easily result from the substrate binding.
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Affiliation(s)
- Leonid T Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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47
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Lemieux MJ, Fischer SJ, Cherney MM, Bateman KS, James MNG. The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc Natl Acad Sci U S A 2007; 104:750-4. [PMID: 17210913 PMCID: PMC1783385 DOI: 10.1073/pnas.0609981104] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Indexed: 11/18/2022] Open
Abstract
Rhomboid peptidases are members of a family of regulated intramembrane peptidases that cleave the transmembrane segments of integral membrane proteins. Rhomboid peptidases have been shown to play a major role in developmental processes in Drosophila and in mitochondrial maintenance in yeast. Most recently, the function of rhomboid peptidases has been directly linked to apoptosis. We have solved the structure of the rhomboid peptidase from Haemophilus influenzae (hiGlpG) to 2.2-A resolution. The phasing for the crystals of hiGlpG was provided mainly by molecular replacement, by using the coordinates of the Escherichia coli rhomboid (ecGlpG). The structural results on these rhomboid peptidases have allowed us to speculate on the catalytic mechanism of substrate cleavage in a membranous environment. We have identified the relative disposition of the nucleophilic serine to the general base/acid function of the conserved histidine. Modeling a tetrapeptide substrate in the context of the rhomboid structure reveals an oxyanion hole comprising the side chain of a second conserved histidine and the main-chain NH of the nucleophilic serine residue. In both hiGlpG and ecGlpG structures, a water molecule occupies this oxyanion hole.
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Affiliation(s)
- M. Joanne Lemieux
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Sarah J. Fischer
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Katherine S. Bateman
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Michael N. G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
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Weidauer E, Yasuda Y, Biswal BK, Cherny M, James MNG, Brömme D. Effects of disease-modifying anti-rheumatic drugs (DMARDs) on the activities of rheumatoid arthritis-associated cathepsins K and S. Biol Chem 2007; 388:331-6. [PMID: 17338641 DOI: 10.1515/bc.2007.037] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rheumatoid arthritis is an inflammatory and disabling joint disease affecting 0.5-1.5% of the population. Although various anti-inflammatory (NSAIDs) and disease-modifying (DMARDs) drugs are in clinical use, their precise mechanisms of action are not always defined. In this report, we discuss the effects of widely used DMARDs such as gold derivatives and chloroquine on cathepsins K and S, which have been implicated as critical mediators of inflammation and joint erosion in rheumatoid arthritis. We demonstrate that clinically potent gold derivatives inhibit cathepsins K and S in in vitro and cell-based assays. An X-ray analysis of the gold thiomalate/cathepsin K complex reveals that the inhibitor is bound to the active-site cysteine residue of the protease. Chloroquine, a lysosomotropic agent of lower clinical potency than gold derivatives, inhibits neutral pH-labile cathepsins intracellularly, but does not affect the neutral pH-stable cathepsin S. The potent inhibition of cathepsins implicated in the pathogenesis of rheumatoid arthritis by gold derivatives may explain the therapeutic efficacy of these drugs.
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Affiliation(s)
- Enrico Weidauer
- Department of Human Genetics, Mount Sinai School of Medicine, New York, NY 10029, USA
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49
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Lee TW, Cherney MM, Liu J, James KE, Powers JC, Eltis LD, James MNG. Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase. J Mol Biol 2006; 366:916-32. [PMID: 17196984 PMCID: PMC7094323 DOI: 10.1016/j.jmb.2006.11.078] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 11/18/2006] [Accepted: 11/28/2006] [Indexed: 01/06/2023]
Abstract
The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.
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Affiliation(s)
- Ting-Wai Lee
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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50
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Garen CR, Cherney MM, Bergmann EM, James MNG. The molecular structure of Rv1873, a conserved hypothetical protein from Mycobacterium tuberculosis, at 1.38 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1201-5. [PMID: 17142896 PMCID: PMC2225384 DOI: 10.1107/s1744309106046902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 11/07/2006] [Indexed: 05/12/2023]
Abstract
The X-ray crystal structure of the gene product encoded by open reading frame Rv1873 of Mycobacterium tuberculosis has been determined by single isomorphous replacement with anomalous scattering (SIRAS) phasing techniques at 1.38 A resolution from monoclinic crystals with unit-cell parameters a = 33.44, b = 31.63, c = 53.19 A, beta = 90.8 degrees. The 16.2 kDa Rv1873 is a monomer that adopts a primarily alpha-helical fold with limited structural similarity to previously determined tertiary structures. It has been annotated as a conserved hypothetical protein of unknown function and is classified by the Clusters of Orthologous Groups (COG) database as belonging to COG5579. The three-dimensional structure of the Rv1873 gene product reveals limited similarity to a repeated motif that is found in a variety of other proteins. While not a novel fold, it serves as a model for orthologues predicted to be related by sequence and it is hoped that knowledge of the structure of Rv1873 will aid in determining a possible function for this protein.
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Affiliation(s)
- Craig R. Garen
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ernst M. Bergmann
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael N. G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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