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Busby JN, Trevelyan S, Pegg CL, Kerr ED, Schulz BL, Chassagnon I, Landsberg MJ, Weston MK, Hurst MRH, Lott JS. The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo. IUCRJ 2024; 11:299-308. [PMID: 38512773 PMCID: PMC11067744 DOI: 10.1107/s2052252524001969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB-TcC subcomplex that makes a hollow shell. This TcB-TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB-TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.
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Affiliation(s)
- Jason N. Busby
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Sarah Trevelyan
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Cassandra L. Pegg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Edward D. Kerr
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Irene Chassagnon
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Michael J. Landsberg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Mitchell K. Weston
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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2
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Usón I, Sheldrick GM. Modes and model building in SHELXE. Acta Crystallogr D Struct Biol 2024; 80:4-15. [PMID: 38088896 PMCID: PMC10833347 DOI: 10.1107/s2059798323010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024] Open
Abstract
Density modification is a standard step to provide a route for routine structure solution by any experimental phasing method, with single-wavelength or multi-wavelength anomalous diffraction being the most popular methods, as well as to extend fragments or incomplete models into a full solution. The effect of density modification on the starting maps from either source is illustrated in the case of SHELXE. The different modes in which the program can run are reviewed; these include less well known uses such as reading external phase values and weights or phase distributions encoded in Hendrickson-Lattman coefficients. Typically in SHELXE, initial phases are calculated from experimental data, from a partial model or map, or from a combination of both sources. The initial phase set is improved and extended by density modification and, if the resolution of the data and the type of structure permits, polyalanine tracing. As a feature to systematically eliminate model bias from phases derived from predicted models, the trace can be set to exclude the area occupied by the starting model. The trace now includes an extension into the gamma position or hydrophobic and aromatic side chains if a sequence is provided, which is performed in every tracing cycle. Once a correlation coefficient of over 30% between the structure factors calculated from such a trace and the native data indicates that the structure has been solved, the sequence is docked in all model-building cycles and side chains are fitted if the map supports it. The extensions to the tracing algorithm brought in to provide a complete model are discussed. The improvement in phasing performance is assessed using a set of tests.
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Affiliation(s)
- Isabel Usón
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, Barcelona, E-08003, Spain
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixach, 15, Barcelona, 08028, Spain
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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3
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Cruz MR, Cristy S, Guha S, De Cesare GB, Evdokimova E, Sanchez H, Borek D, Miramón P, Yano J, Fidel PL, Savchenko A, Andes DR, Stogios PJ, Lorenz MC, Garsin DA. Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against fungal infections. Nat Commun 2022; 13:6047. [PMID: 36229448 PMCID: PMC9562342 DOI: 10.1038/s41467-022-33613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023] Open
Abstract
Fungal pathogens are a continuing challenge due to few effective antifungals and a rise in resistance. In previous work, we described the inhibition of Candida albicans virulence following exposure to the 68 amino acid bacteriocin, EntV, secreted by Enterococcus faecalis. Here, to optimize EntV as a potential therapeutic and better understand its antifungal features, an X-ray structure is obtained. The structure consists of six alpha helices enclosing a seventh 16 amino acid helix (α7). The individual helices are tested for antifungal activity using in vitro and nematode infection assays. Interestingly, α7 retains antifungal, but not antibacterial activity and is also effective against Candida auris and Cryptococcus neoformans. Further reduction of α7 to 12 amino acids retains full antifungal activity, and excellent efficacy is observed in rodent models of C. albicans oropharyngeal, systemic, and venous catheter infections. Together, these results showcase EntV-derived peptides as promising candidates for antifungal therapeutic development.
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Affiliation(s)
- Melissa R. Cruz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shane Cristy
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shantanu Guha
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Giuseppe Buda De Cesare
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Elena Evdokimova
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Hiram Sanchez
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Dominika Borek
- grid.267313.20000 0000 9482 7121Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Pedro Miramón
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Junko Yano
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Paul L. Fidel
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Alexei Savchenko
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada ,grid.22072.350000 0004 1936 7697Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada ,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL USA
| | - David R. Andes
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Peter J. Stogios
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Michael C. Lorenz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Danielle A. Garsin
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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4
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Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W. The induction mechanism of the flavonoid-responsive regulator FrrA. FEBS J 2022; 289:507-518. [PMID: 34314575 DOI: 10.1111/febs.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation-promoting genetic programme in the presence of host-produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid-responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR-like fold whose DNA-binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C-H contacts to the π-system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA-binding domain and the absence of structural change upon ligand binding are corroborated by small-angle X-ray scattering (SAXS) experiments in solution. Together with a model of the promoter-bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA-binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.
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Affiliation(s)
- Nadine Werner
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Sebastiaan Werten
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Jens Hoppen
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Gottfried J Palm
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Michael Göttfert
- Institute of Genetics, Dresden University of Technology, Germany
| | - Winfried Hinrichs
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
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5
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Mehta N, Maddineni S, Mathews II, Andres Parra Sperberg R, Huang PS, Cochran JR. Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation. Cell Rep 2020; 28:2509-2516.e5. [PMID: 31484064 DOI: 10.1016/j.celrep.2019.07.073] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
V-domain immunoglobulin (Ig) suppressor of T cell activation (VISTA) is an immune checkpoint protein that inhibits the T cell response against cancer. Similar to PD-1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Here, we report a 1.85 Å crystal structure of the elusive human VISTA extracellular domain, whose lack of homology necessitated a combinatorial MR-Rosetta approach for structure determination. We highlight features that make the VISTA immunoglobulin variable (IgV)-like fold unique among B7 family members, including two additional disulfide bonds and an extended loop region with an attached helix that we show forms a contiguous binding epitope for a clinically relevant anti-VISTA antibody. We propose an overlap of this antibody-binding region with the binding epitope for V-set and Ig domain containing 3 (VSIG3), a purported functional binding partner of VISTA. The structure and functional epitope presented here will help guide future drug development efforts against this important checkpoint target.
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Affiliation(s)
- Nishant Mehta
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Irimpan I Mathews
- Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
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6
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Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2: Structure and Catalytic Mechanism. Appl Environ Microbiol 2020; 86:AEM.02971-19. [PMID: 32303545 DOI: 10.1128/aem.02971-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/07/2020] [Indexed: 01/24/2023] Open
Abstract
Carboxylesterase PytH, isolated from the pyrethroid-degrading bacterium Sphingobium faniae JZ-2, could rapidly hydrolyze the ester bond of a wide range of pyrethroid pesticides, including permethrin, fenpropathrin, cypermethrin, fenvalerate, deltamethrin, cyhalothrin, and bifenthrin. To elucidate the catalytic mechanism of PytH, we report here the crystal structures of PytH with bifenthrin (BIF) and phenylmethylsulfonyl fluoride (PMSF) and two PytH mutants. Though PytH shares low sequence identity with reported α/β-hydrolase fold proteins, the typical triad catalytic center with Ser-His-Asp triad (Ser78, His230, and Asp202) is present and vital for the hydrolase activity. However, no contact was found between Ser78 and His230 in the structures we solved, which may be due to the fact that the PytH structures we determined are in their inactive or low-activity forms. The structure of PytH is composed of a core domain and a lid domain; some hydrophobic amino acid residues surrounding the substrate from both domains form a deeper and wider hydrophobic pocket than its homologous structures. This indicates that the larger hydrophobic pocket makes PytH fit for its larger substrate binding; both lid and core domains are involved in substrate binding, and the lid domain-induced core domain movement may make the active center correctly positioned with substrates.IMPORTANCE Pyrethroid pesticides are widely applied in agriculture and household; however, extensive use of these pesticides also causes serious environmental and health problems. The hydrolysis of pyrethroids by carboxylesterases is the major pathway of microbial degradation of pyrethroids, but the structure of carboxylesterases and its catalytic mechanism are still unknown. Carboxylesterase PytH from Sphingobium faniae JZ-2 could effectively hydrolyze a wide range of pyrethroid pesticides. The crystal structures of PytH are solved in this study. This showed that PytH belongs to the α/β-hydrolase fold proteins with typical catalytic Ser-His-Asp triad, though PytH has a low sequence identity (about 20%) with them. The special large hydrophobic binding pocket enabled PytH to bind bigger pyrethroid family substrates. Our structures shed light on the substrate selectivity and the future application of PytH and deepen our understanding of α/β-hydrolase members.
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7
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Minici C, Mosca L, Ilisso CP, Cacciapuoti G, Porcelli M, Degano M. Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues. J Struct Biol 2020; 210:107462. [PMID: 31962159 DOI: 10.1016/j.jsb.2020.107462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/21/2023]
Abstract
Methionine adenosyltransferases catalyse the biosynthesis of S-adenosylmethionine, the primary methyl group donor in biochemical reactions, through the condensation of methionine and ATP. Here, we report the structural analysis of the Pyrococcus furiosus methionine adenosyltransferase (PfMAT) captured in the unliganded, substrate- and product-bound states. The conformational changes taking place during the enzymatic catalytic cycle are allosterically propagated by amino acid residues conserved in the archaeal orthologues to induce an asymmetric dimer structure. The distinct occupancy of the active sites within a PfMAT dimer is consistent with a half-site reactivity that is mediated by a product-induced negative cooperativity. The structures of intermediate states of PfMAT reported here suggest a distinct molecular mechanism for S-adenosylmethionine synthesis in Archaea, likely consequence of the evolutionary pressure to achieve protein stability under extreme conditions.
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Affiliation(s)
- Claudia Minici
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy
| | - Laura Mosca
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Concetta Paola Ilisso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna Cacciapuoti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marina Porcelli
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy.
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8
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Structural consequences of BMPR2 kinase domain mutations causing pulmonary arterial hypertension. Sci Rep 2019; 9:18351. [PMID: 31797984 PMCID: PMC6892941 DOI: 10.1038/s41598-019-54830-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/14/2019] [Indexed: 11/09/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) are secreted ligands of the transforming growth factor-β (TGF-β) family that control embryonic patterning, as well as tissue development and homeostasis. Loss of function mutations in the type II BMP receptor BMPR2 are the leading cause of pulmonary arterial hypertension (PAH), a rare disease of vascular occlusion that leads to high blood pressure in the pulmonary arteries. To understand the structural consequences of these mutations, we determined the crystal structure of the human wild-type BMPR2 kinase domain at 2.35 Å resolution. The structure revealed an active conformation of the catalytic domain that formed canonical interactions with the bound ligand Mg-ADP. Disease-associated missense mutations were mapped throughout the protein structure, but clustered predominantly in the larger kinase C-lobe. Modelling revealed that the mutations will destabilize the protein structure by varying extents consistent with their previously reported functional heterogeneity. The most severe mutations introduced steric clashes in the hydrophobic protein core, whereas those found on the protein surface were less destabilizing and potentially most favorable for therapeutic rescue strategies currently under clinical investigation.
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9
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Sharma M, Kumar V. Crystal structure of BinAB toxin receptor (Cqm1) protein and molecular dynamics simulations reveal the role of unique Ca(II) ion. Int J Biol Macromol 2019; 140:1315-1325. [PMID: 31449868 DOI: 10.1016/j.ijbiomac.2019.08.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin that is used world-wide for control of the mosquito population. The protein was crystallized in the presence of a mixture of divalent metal ions. Cqm1 crystal structure was solved using the MRSAD method using Cd(II) anomalous at 1.9 Å wavelength and the structure was refined against 1.8 Å synchrotron data. One tightly bound Ca(II) ion in each of the monomer was observed and this site is suggested here to be unique to the GH13_17 family. Molecular dynamics simulations provide clues for the functional role of Ca(II) ion shown earlier to be essential for enzymatic activity. An optimized substrate (maltotriose) bound structure of the complex was constructed based on which 'retaining-type' mechanism can be predicted reliably. It reveals large conformational change in aromatic residues situated at active-site entrance. A Cd(II) ion was observed overlapping with the substrate-binding site. Kinetics data suggests non-competitive inhibition of Cqm1 by Cd(II). This is the first structure from the GH13_17 family and provides template for constructing reliable models for other members.
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Affiliation(s)
- Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Vinay Kumar
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India.
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10
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Lin KF, Hsu JY, Hsieh DL, Tsai MJ, Yeh CH, Chen CY. Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus. Acta Crystallogr F Struct Biol Commun 2019; 75:73-79. [PMID: 30713157 PMCID: PMC6360439 DOI: 10.1107/s2053230x18017673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/13/2018] [Indexed: 11/10/2022] Open
Abstract
Programmed cell death 5 (PDCD5) is a vital signaling protein in the apoptosis pathway in eukaryotes. It is known that there are two dissociated N-terminal regions and a triple-helix core in eukaryotic PDCD5. Structural and functional studies of PDCD5 from hyperthermophilic archaea have been limited to date. Here, the PDCD5 homolog Sso0352 (SsoPDCD5) was identified in Sulfolobus solfataricus, the SsoPDCD5 protein was expressed and crystallized, and the phase was identified by single-wavelength anomalous diffraction. The native SsoPDCD5 crystal belonged to space group C2 and diffracted to 1.49 Å resolution. This is the first crystal structure of a PDCD5 homolog to be solved. SsoPDCD5 shares a similar triple-helix bundle with eukaryotic PDCD5 but has a long α-helix in the N-terminus. A structural search and biochemical data suggest that SsoPDCD5 may function as a DNA-binding protein.
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Affiliation(s)
- Kuan-Fu Lin
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Jia-Yuan Hsu
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Dong-Lin Hsieh
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Meng-Ju Tsai
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Ching-Hui Yeh
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan
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11
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Rolig AS, Sweeney EG, Kaye LE, DeSantis MD, Perkins A, Banse AV, Hamilton MK, Guillemin K. A bacterial immunomodulatory protein with lipocalin-like domains facilitates host-bacteria mutualism in larval zebrafish. eLife 2018; 7:37172. [PMID: 30398151 PMCID: PMC6219842 DOI: 10.7554/elife.37172] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Stable mutualism between a host and its resident bacteria requires a moderated immune response to control bacterial population size without eliciting excessive inflammation that could harm both partners. Little is known about the specific molecular mechanisms utilized by bacterial mutualists to temper their hosts' responses and protect themselves from aggressive immune attack. Using a gnotobiotic larval zebrafish model, we identified an Aeromonas secreted immunomodulatory protein, AimA. AimA is required during colonization to prevent intestinal inflammation that simultaneously compromises both bacterial and host survival. Administration of exogenous AimA prevents excessive intestinal neutrophil accumulation and protects against septic shock in models of both bacterially and chemically induced intestinal inflammation. We determined the molecular structure of AimA, which revealed two related calycin-like domains with structural similarity to the mammalian immune modulatory protein, lipocalin-2. As a secreted bacterial protein required by both partners for optimal fitness, AimA is an exemplar bacterial mutualism factor.
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Affiliation(s)
- Annah S Rolig
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Lila E Kaye
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Michael D DeSantis
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Allison V Banse
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, United States.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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12
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Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Proc Natl Acad Sci U S A 2017; 115:168-173. [PMID: 29255041 PMCID: PMC5776812 DOI: 10.1073/pnas.1715471115] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Circulating influenza viruses evade neutralization in their human hosts by acquiring escape mutations at epitopes of prevalent antibodies. A goal for next-generation influenza vaccines is to reduce escape likelihood by selectively eliciting antibodies recognizing conserved surfaces on the viral hemagglutinin (HA). The receptor-binding site (RBS) on the HA "head" and a region near the fusion peptide on the HA "stem" are two such sites. We describe here a human antibody clonal lineage, designated CL6649, members of which bind a third conserved site ("lateral patch") on the side of the H1-subtype, HA head. A crystal structure of HA with bound Fab6649 shows the conserved antibody footprint. The site was invariant in isolates from 1977 (seasonal) to 2012 (pdm2009); antibodies in CL6649 recognize HAs from the entire period. In 2013, human H1 viruses acquired mutations in this epitope that were retained in subsequent seasons, prompting modification of the H1 vaccine component in 2017. The mutations inhibit Fab6649 binding. We infer from the rapid spread of these mutations in circulating H1 influenza viruses that the previously subdominant, conserved lateral patch had become immunodominant for individuals with B-cell memory imprinted by earlier H1 exposure. We suggest that introduction of the pdm2009 H1 virus, to which most of the broadly prevalent, neutralizing antibodies did not bind, conferred a selective advantage in the immune systems of infected hosts to recall of memory B cells that recognized the lateral patch, the principal exposed epitope that did not change when pdm2009 displaced previous seasonal H1 viruses.
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13
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Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii. Nat Commun 2017; 8:1336. [PMID: 29109439 PMCID: PMC5673888 DOI: 10.1038/s41467-017-01399-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/13/2017] [Indexed: 01/17/2023] Open
Abstract
The MacA-MacB-TolC tripartite complex is a transmembrane machine that spans both plasma membrane and outer membrane and actively extrudes substrates, including macrolide antibiotics, virulence factors, peptides and cell envelope precursors. These transport activities are driven by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. Here, we present the crystal structure of MacB at 3.4-Å resolution. MacB forms a dimer in which each protomer contains a nucleotide-binding domain and four transmembrane helices that protrude in the periplasm into a binding domain for interaction with the membrane fusion protein MacA. MacB represents an ABC transporter in pathogenic microorganisms with unique structural features.
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14
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Chatterjee S, Luthra P, Esaulova E, Agapov E, Yen BC, Borek DM, Edwards MR, Mittal A, Jordan DS, Ramanan P, Moore ML, Pappu RV, Holtzman MJ, Artyomov MN, Basler CF, Amarasinghe GK, Leung DW. Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses. Nat Microbiol 2017; 2:17101. [PMID: 28665409 DOI: 10.1038/nmicrobiol.2017.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Human respiratory syncytial virus (hRSV) is a major cause of morbidity and mortality in the paediatric, elderly and immune-compromised populations1,2. A gap in our understanding of hRSV disease pathology is the interplay between virally encoded immune antagonists and host components that limit hRSV replication. hRSV encodes for non-structural (NS) proteins that are important immune antagonists3-6; however, the role of these proteins in viral pathogenesis is incompletely understood. Here, we report the crystal structure of hRSV NS1 protein, which suggests that NS1 is a structural paralogue of hRSV matrix (M) protein. Comparative analysis of the shared structural fold with M revealed regions unique to NS1. Studies on NS1 wild type or mutant alone or in recombinant RSVs demonstrate that structural regions unique to NS1 contribute to modulation of host responses, including inhibition of type I interferon responses, suppression of dendritic cell maturation and promotion of inflammatory responses. Transcriptional profiles of A549 cells infected with recombinant RSVs show significant differences in multiple host pathways, suggesting that NS1 may have a greater role in regulating host responses than previously appreciated. These results provide a framework to target NS1 for therapeutic development to limit hRSV-associated morbidity and mortality.
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Affiliation(s)
- Srirupa Chatterjee
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA.,Computer Technologies Department, ITMO University, Saint Petersburg 197101, Russia
| | - Eugene Agapov
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Benjamin C Yen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dominika M Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Texas 75390, USA
| | - Megan R Edwards
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - David S Jordan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Parameshwar Ramanan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Martin L Moore
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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15
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Guerra P, Valbuena A, Querol-Audí J, Silva C, Castellanos M, Rodríguez-Huete A, Garriga D, Mateu MG, Verdaguer N. Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations. Sci Rep 2017; 7:4101. [PMID: 28642465 PMCID: PMC5481337 DOI: 10.1038/s41598-017-04345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022] Open
Abstract
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics. To provide atomic-resolution insights into biologically relevant changes in virus capsid mechanics, we have determined by X-ray crystallography the structural effects of deleterious, mechanically stiffening mutations around the capsid pores. Data show that the cavity-creating N170A mutation at the pore wall does not induce any dramatic structural change around the pores, but instead generates subtle rearrangements that propagate throughout the capsid, resulting in a more compact, less flexible structure. Analysis of the spacefilling L172W mutation revealed the same relationship between increased stiffness and compacted capsid structure. Implications for understanding connections between virus mechanics, structure, dynamics and infectivity, and for engineering modified virus-based nanoparticles, are discussed.
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Affiliation(s)
- Pablo Guerra
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jordi Querol-Audí
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Cristina Silva
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Damià Garriga
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain.
| | - Nuria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain.
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16
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Brautigam CA, Deka RK, Liu WZ, Tomchick DR, Norgard MV. Functional clues from the crystal structure of an orphan periplasmic ligand-binding protein from Treponema pallidum. Protein Sci 2017; 26:847-856. [PMID: 28168761 DOI: 10.1002/pro.3133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/01/2023]
Abstract
The spirochete Treponema pallidum is the causative agent of syphilis, a sexually transmitted infection of major global importance. Other closely related subspecies of Treponema also are the etiological agents of the endemic treponematoses, such as yaws, pinta, and bejel. The inability of T. pallidum and its close relatives to be cultured in vitro has prompted efforts to characterize T. pallidum's proteins structurally and biophysically, particularly those potentially relevant to treponemal membrane biology, with the goal of possibly revealing the functions of those proteins. This report describes the structure of the treponemal protein Tp0737; this polypeptide has a fold characteristic of a class of periplasmic ligand-binding proteins associated with ABC-type transporters. Although no ligand for the protein was observed in electron-density maps, and thus the nature of the native ligand remains obscure, the structural data described herein provide a foundation for further efforts to elucidate the ligand and thus the function of this protein in T. pallidum.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Ranjit K Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Wei Z Liu
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Diana R Tomchick
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Michael V Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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17
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Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. Sci Rep 2017; 7:44103. [PMID: 28272521 PMCID: PMC5341072 DOI: 10.1038/srep44103] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/01/2017] [Indexed: 11/29/2022] Open
Abstract
Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.
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Affiliation(s)
- Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Tran Hai
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Anatoly Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Mahbod Hajighasemi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Julia Glinos
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | | | - Veronica Yim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Thomas Brüls
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique, Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS), UMR8030, Génomique métabolique, Evry, France
| | - Denis Le Paslier
- Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche, Scientifique (CNRS), UMR8030, Génomique métabolique, Commissariat à l'Energie, Atomique et aux Energies Alternatives (CEA), Direction de la Recherche, Fondamentale, Institut de Génomique, Evry, France
| | | | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | | | - Olga V Golyshina
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
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18
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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA. PLoS One 2017; 12:e0169627. [PMID: 28068385 PMCID: PMC5222340 DOI: 10.1371/journal.pone.0169627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022] Open
Abstract
The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.
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19
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Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain. Nat Med 2016; 22:1465-1469. [PMID: 27820604 DOI: 10.1038/nm.4223] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022]
Abstract
For broad protection against infection by viruses such as influenza or HIV, vaccines should elicit antibodies that bind conserved viral epitopes, such as the receptor-binding site (RBS). RBS-directed antibodies have been described for both HIV and influenza virus, and the design of immunogens to elicit them is a goal of vaccine research in both fields. Residues in the RBS of influenza virus hemagglutinin (HA) determine a preference for the avian or human receptor, α-2,3-linked sialic acid and α-2,6-linked sialic acid, respectively. Transmission of an avian-origin virus between humans generally requires one or more mutations in the sequences encoding the influenza virus RBS to change the preferred receptor from avian to human, but passage of a human-derived vaccine candidate in chicken eggs can select for reversion to avian receptor preference. For example, the X-181 strain of the 2009 new pandemic H1N1 influenza virus, derived from the A/California/07/2009 isolate and used in essentially all vaccines since 2009, has arginine at position 226, a residue known to confer preference for an α-2,3 linkage in H1 subtype viruses; the wild-type A/California/07/2009 isolate, like most circulating human H1N1 viruses, has glutamine at position 226. We describe, from three different individuals, RBS-directed antibodies that recognize the avian-adapted H1 strain in current influenza vaccines but not the circulating new pandemic 2009 virus; Arg226 in the vaccine-strain RBS accounts for the restriction. The polyclonal sera of the three donors also reflect this preference. Therefore, when vaccines produced from strains that are never passaged in avian cells become widely available, they may prove more capable of eliciting RBS-directed, broadly neutralizing antibodies than those produced from egg-adapted viruses, extending the established benefits of current seasonal influenza immunizations.
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20
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Sánchez-Eugenia R, Durana A, López-Marijuan I, Marti GA, Guérin DMA. X-ray structure of Triatoma virus empty capsid: insights into the mechanism of uncoating and RNA release in dicistroviruses. J Gen Virol 2016; 97:2769-2779. [DOI: 10.1099/jgv.0.000580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rubén Sánchez-Eugenia
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Aritz Durana
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Ibai López-Marijuan
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Gerardo A. Marti
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT-La Plata-CONICET-UNLP), Boulevard 120 e/61 y 62, 1900 La Plata, Argentina
| | - Diego M. A. Guérin
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
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21
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Brautigam CA, Deka RK, Liu WZ, Norgard MV. The Tp0684 (MglB-2) Lipoprotein of Treponema pallidum: A Glucose-Binding Protein with Divergent Topology. PLoS One 2016; 11:e0161022. [PMID: 27536942 PMCID: PMC4990184 DOI: 10.1371/journal.pone.0161022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022] Open
Abstract
Treponema pallidum, the bacterium that causes syphilis, is an obligate human parasite. As such, it must acquire energy, in the form of carbon sources, from the host. There is ample evidence that the principal source of energy for this spirochete is D-glucose acquired from its environment, likely via an ABC transporter. Further, there is genetic evidence of a D-glucose chemotaxis system in T. pallidum. Both of these processes may be dependent on a single lipidated chemoreceptor: Tp0684, also called TpMglB-2 for its sequence homology to MglB of Escherichia coli. To broaden our understanding of this potentially vital protein, we determined a 2.05-Å X-ray crystal structure of a soluble form of the recombinant protein. Like its namesake, TpMglB-2 adopts a bilobed fold that is similar to that of the ligand-binding proteins (LBPs) of other ABC transporters. However, the protein has an unusual, circularly permuted topology. This feature prompted a series of biophysical studies that examined whether the protein's topological distinctiveness affected its putative chemoreceptor functions. Differential scanning fluorimetry and isothermal titration calorimetry were used to confirm that the protein bound D-glucose in a cleft between its two lobes. Additionally, analytical ultracentrifugation was employed to reveal that D-glucose binding is accompanied by a significant conformational change. TpMglB-2 thus appears to be fully functional in vitro, and given the probable central importance of the protein to T. pallidum's physiology, our results have implications for the viability and pathogenicity of this obligate human pathogen.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Ranjit K. Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Wei Z. Liu
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
| | - Michael V. Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, United States of America
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22
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Abstract
This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.
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Affiliation(s)
- G N Murshudov
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
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23
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Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature 2016; 533:561-4. [PMID: 27144356 DOI: 10.1038/nature17666] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/15/2016] [Indexed: 02/08/2023]
Abstract
ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral sterols in liver and intestines. Mutations disrupting G5G8 cause sitosterolaemia, a disorder characterized by sterol accumulation and premature atherosclerosis. Here we use crystallization in lipid bilayers to determine the X-ray structure of human G5G8 in a nucleotide-free state at 3.9 Å resolution, generating the first atomic model of an ABC sterol transporter. The structure reveals a new transmembrane fold that is present in a large and functionally diverse superfamily of ABC transporters. The transmembrane domains are coupled to the nucleotide-binding sites by networks of interactions that differ between the active and inactive ATPases, reflecting the catalytic asymmetry of the transporter. The G5G8 structure provides a mechanistic framework for understanding sterol transport and the disruptive effects of mutations causing sitosterolaemia.
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24
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Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034702. [PMID: 27191010 PMCID: PMC4851618 DOI: 10.1063/1.4948539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
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Affiliation(s)
- Hongnan Cao
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Lance Bigelow
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Robert Jedrzejczak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Gyorgy Babnigg
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Madan K Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Shanteri Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - George N Phillips
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
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25
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Wang W, Yan R, Nocek BP, Vuong TV, Di Leo R, Xu X, Cui H, Gatenholm P, Toriz G, Tenkanen M, Savchenko A, Master ER. Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T. J Biol Chem 2016; 291:14120-14133. [PMID: 27129264 DOI: 10.1074/jbc.m115.702944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/01/2023] Open
Abstract
Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups. Herein, a family GH115 enzymefrom the marine bacterium Saccharophagus degradans 2-40(T), SdeAgu115A, demonstrated activity toward glucuronoxylan and oligomers thereof with preference toward MeGlcAp linked to internal xylopyranosyl residues. Unique biochemical characteristics of NaCl activation were also observed. The crystal structure of SdeAgu115A revealed a five-domain architecture, with an additional insertion C(+) domain that had significant impact on the domain arrangement of SdeAgu115A monomer and its dimerization. The participation of domain C(+) in substrate binding was supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp-335, the catalytic essentiality of Glu-216 was revealed by site-specific mutagenesis. A primary sequence analysis suggested that the SdeAgu115A architecture is shared by more than half of GH115 members, thus defining a distinct archetype for GH115 enzymes.
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Affiliation(s)
- Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Boguslaw P Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Paul Gatenholm
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg 412 96, Sweden
| | - Guillermo Toriz
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg 412 96, Sweden,; Department of Wood, Cellulose and Paper Research, University of Guadalajara, Guadalajara 44100, Mexico
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada,.
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada,.
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26
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Martinelli L, García-Morales L, Querol E, Piñol J, Fita I, Calisto BM. Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium. PLoS Pathog 2016; 12:e1005533. [PMID: 27082435 PMCID: PMC4833410 DOI: 10.1371/journal.ppat.1005533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
The emergent human pathogen Mycoplasma genitalium, with one of the smallest genomes among cells capable of growing in axenic cultures, presents a flask-shaped morphology due to a protrusion of the cell membrane, known as the terminal organelle, that is involved in cell adhesion and motility and is an important virulence factor of this microorganism. The terminal organelle is supported by a cytoskeleton complex of about 300 nm in length that includes three substructures: the terminal button, the rod and the wheel complex. The crystal structure of the MG491 protein, a proposed component of the wheel complex, has been determined at ~3 Å resolution. MG491 subunits are composed of a 60-residue N-terminus, a central three-helix-bundle spanning about 150 residues and a C-terminal region that appears to be quite flexible and contains the region that interacts with MG200, another key protein of the terminal organelle. The MG491 molecule is a tetramer presenting a unique organization as a dimer of asymmetric pairs of subunits. The asymmetric arrangement results in two very different intersubunit interfaces between the central three-helix-bundle domains, which correlates with the formation of only ~50% of the intersubunit disulfide bridges of the single cysteine residue found in MG491 (Cys87). Moreover, M. genitalium cells with a point mutation in the MG491 gene causing the change of Cys87 to Ser present a drastic reduction in motility (as determined by microcinematography) and important alterations in morphology (as determined by electron microscopy), while preserving normal levels of the terminal organelle proteins. Other variants of MG491, designed also according to the structural information, altered significantly the motility and/or the cell morphology. Together, these results indicate that MG491 plays a key role in the functioning, organization and stabilization of the terminal organelle.
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Affiliation(s)
- Luca Martinelli
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Luis García-Morales
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Bárbara M. Calisto
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, Grenoble, France and Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- * E-mail:
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27
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Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun 2016; 7:10175. [PMID: 26729507 PMCID: PMC4728340 DOI: 10.1038/ncomms10175] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/11/2015] [Indexed: 11/08/2022] Open
Abstract
The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0 Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Oliver B. Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - David Tomasek
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Habon A. Issa
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Desiree C. von Alpen
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Heather L. Pond
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Surajit Banerjee
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Qun Liu
- New York Structural Biology Center, X4 Beamlines, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chijun Li
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Edda Kloppmann
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - M. Chiara Manzini
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
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28
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Wallen JR, Mallett TC, Okuno T, Parsonage D, Sakai H, Tsukihara T, Claiborne A. Structural Analysis of Streptococcus pyogenes NADH Oxidase: Conformational Dynamics Involved in Formation of the C(4a)-Peroxyflavin Intermediate. Biochemistry 2015; 54:6815-29. [PMID: 26506002 DOI: 10.1021/acs.biochem.5b00676] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In probing the oxygen reactivity of an Enterococcus faecalis NADH oxidase (Nox; O2 → 2H2O) C42S mutant lacking the Cys42-sulfenic acid (Cys42-SOH) redox center, we provided direct evidence of a C(4a)-peroxyflavin intermediate in the oxidative half-reaction and also described a conformational or chemical change that is rate-limiting for full reoxidation of the homodimer. In this work, the Nox from Streptococcus pyogenes (SpyNox) has been expressed and crystallized, and the overoxidized wild-type [Cys44-SOH → Cys44-sulfinic acid (Cys44-SO2H)] and C44S mutant enzyme structures have been refined at 2.0 and 2.15 Å, respectively. We show that azide binds to the two-electron reduced wild-type (EH2) enzyme and to the mutant enzyme in solution, but with a significantly higher affinity for the mutant protein. The spectral course of the titration with the SpyNox EH2 form clearly indicates progressive displacement of the Cys44-S(-) → FAD charge-transfer interaction. An azide soak with C44S Nox crystals led to the structure of the complex, as refined at 2.10 Å. The active-site N3(-) ligand is proximal to the Ser44 and His11 side chains, and a significant shift in the Ser44 side chain also appears. This provides an attractive explanation for the azide-induced loss of charge-transfer absorbance seen with the wild-type EH2 form and also permits accommodation of a C(4a)-peroxyflavin structural model. The conformation of Ser44 and the associated helical element, and the resulting steric accommodation, appear to be linked to the conformational change described in the E. faecalis C42S Nox oxidative half-reaction.
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Affiliation(s)
- Jamie R Wallen
- Department of Chemistry and Physics, Western Carolina University , Cullowhee, North Carolina 28723, United States
| | - T Conn Mallett
- Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina 27157, United States
| | - Takashi Okuno
- Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina 27157, United States
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina 27157, United States
| | - Hiroaki Sakai
- Institute for Protein Research, Osaka University , Suita, Osaka 565-0871, Japan
| | - Tomitake Tsukihara
- Institute for Protein Research, Osaka University , Suita, Osaka 565-0871, Japan
| | - Al Claiborne
- Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina 27157, United States
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29
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Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei AR, Sung P, Xiong Y. The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Nat Commun 2015; 5:2987. [PMID: 24390579 DOI: 10.1038/ncomms3987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 11/21/2013] [Indexed: 01/07/2023] Open
Abstract
The conserved MHF1-MHF2 (MHF) complex functions in the activation of the Fanconi anaemia pathway of the DNA damage response, in regulating homologous recombination, and in DNA replication fork maintenance. MHF facilitates the processing of multiple types of branched DNAs by the DNA translocase FANCM. Here we report the crystal structure of a human MHF-DNA complex that reveals the DNA-binding mode of MHF. The structure suggests that MHF prefers branched DNA over double-stranded DNA because it engages two duplex arms. Biochemical analyses verify that MHF preferentially engages DNA forks or various four-way junctions independent of the junction-site structure. Furthermore, genetic experiments provide evidence that the observed DNA-binding interface of MHF is important for cellular resistance to DNA damage. These results offer insights into how the MHF complex recognizes branched DNA and stimulates FANCM activity at such a structure to promote genome maintenance.
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Affiliation(s)
- Qi Zhao
- 1] Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2]
| | - Dorina Saro
- 1] Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2]
| | - Aristidis Sachpatzidis
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Thiyam Ramsing Singh
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation and University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Daniel Schlingman
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiao-Feng Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Andrew Mack
- Department of Applied Physics, Yale University, New Haven, Connecticut 06511, USA
| | - Miaw-Sheue Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Simon Mochrie
- 1] Department of Applied Physics, Yale University, New Haven, Connecticut 06511, USA [2] Department of Physics, Yale University, New Haven, Connecticut 06511, USA
| | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Amom Ruhikanta Meetei
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation and University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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30
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Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One 2015; 10:e0128700. [PMID: 26039067 PMCID: PMC4454674 DOI: 10.1371/journal.pone.0128700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/29/2015] [Indexed: 11/20/2022] Open
Abstract
Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.
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31
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Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NGJ. Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc 2015; 137:6947-55. [PMID: 25961938 DOI: 10.1021/jacs.5b03482] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.
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32
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Leung DW, Borek D, Luthra P, Binning JM, Anantpadma M, Liu G, Harvey IB, Su Z, Endlich-Frazier A, Pan J, Shabman RS, Chiu W, Davey RA, Otwinowski Z, Basler CF, Amarasinghe GK. An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions. Cell Rep 2015; 11:376-89. [PMID: 25865894 DOI: 10.1016/j.celrep.2015.03.034] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/18/2015] [Accepted: 03/12/2015] [Indexed: 01/19/2023] Open
Abstract
During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
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Affiliation(s)
- Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Dominika Borek
- Departments of Biophysics and Biochemistry and Center for Structural Genomics of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Priya Luthra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jennifer M Binning
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Gai Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Ian B Harvey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ariel Endlich-Frazier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juanli Pan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Reed S Shabman
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry and Center for Structural Genomics of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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33
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Zhao Q, Xue X, Longerich S, Sung P, Xiong Y. Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer. Nat Commun 2014; 5:5726. [PMID: 25500724 PMCID: PMC4268874 DOI: 10.1038/ncomms6726] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/30/2014] [Indexed: 12/01/2022] Open
Abstract
Human FANCD2-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). FAN1 maintains genomic stability and prevents tissue decline in multiple organs, yet it confers ICL-induced anti-cancer drug resistance in several cancer subtypes. Here we report three crystal structures of human FAN1 in complex with a 5′ flap DNA substrate, showing that two FAN1 molecules form a head-to-tail dimer to locate the lesion, orient the DNA and unwind a 5′ flap for subsequent incision. Biochemical experiments further validate our model for FAN1 action, as structure-informed mutations that disrupt protein dimerization, substrate orientation or flap unwinding impair the structure-specific nuclease activity. Our work elucidates essential aspects of FAN1-DNA lesion recognition and a unique mechanism of incision. These structural insights shed light on the cellular mechanisms underlying organ degeneration protection and cancer drug resistance mediated by FAN1. FAN1 is a structure-specific nuclease that plays a major role in eliminating highly cytotoxic interstrand DNA crosslinks. Here, Zhao et al. present several crystal structures of FAN1 in complex with DNA substrates and biochemical analyses that establish how FAN1 functions to resolve interstrand DNA crosslinks.![]()
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Affiliation(s)
- Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Simonne Longerich
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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34
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Tucker AC, Taylor KC, Rank KC, Rayment I, Escalante-Semerena JC. Insights into the specificity of lysine acetyltransferases. J Biol Chem 2014; 289:36249-62. [PMID: 25381442 DOI: 10.1074/jbc.m114.613901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reversible lysine acetylation by protein acetyltransferases is a conserved regulatory mechanism that controls diverse cellular pathways. Gcn5-related N-acetyltransferases (GNATs), named after their founding member, are found in all domains of life. GNATs are known for their role as histone acetyltransferases, but non-histone bacterial protein acetytransferases have been identified. Only structures of GNAT complexes with short histone peptide substrates are available in databases. Given the biological importance of this modification and the abundance of lysine in polypeptides, how specificity is attained for larger protein substrates is central to understanding acetyl-lysine-regulated networks. Here we report the structure of a GNAT in complex with a globular protein substrate solved to 1.9 Å. GNAT binds the protein substrate with extensive surface interactions distinct from those reported for GNAT-peptide complexes. Our data reveal determinants needed for the recognition of a protein substrate and provide insight into the specificity of GNATs.
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Affiliation(s)
- Alex C Tucker
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602 and
| | - Keenan C Taylor
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Katherine C Rank
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Ivan Rayment
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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Brautigam CA, Deka RK, Liu WZ, Norgard MV. Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses. Protein Sci 2014; 24:11-9. [PMID: 25287511 DOI: 10.1002/pro.2576] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/30/2014] [Indexed: 12/15/2022]
Abstract
The sexually transmitted disease syphilis is caused by the bacterial spirochete Treponema pallidum. This microorganism is genetically intractable, accounting for the large number of putative and undercharacterized members of the pathogen's proteome. In an effort to ascribe a function(s) to the TP0435 (Tp17) lipoprotein, we engineered a soluble variant of the protein (rTP0435) and determined its crystal structure at a resolution of 2.42 Å. The structure is characterized by an eight-stranded β-barrel protein with a shallow "basin" at one end of the barrel and an α-helix stacked on the opposite end. Furthermore, there is a disulfide-linked dimer of the protein in the asymmetric unit of the crystals. Solution hydrodynamic experiments established that purified rTP0435 is monomeric, but specifically forms the disulfide-stabilized dimer observed in the crystal structure. The data herein, when considered with previous work on TP0435, imply plausible roles for the protein in either ligand binding, treponemal membrane architecture, and/or pathogenesis.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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The Vanadium Iodoperoxidase from the marine flavobacteriaceae species Zobellia galactanivorans reveals novel molecular and evolutionary features of halide specificity in the vanadium haloperoxidase enzyme family. Appl Environ Microbiol 2014; 80:7561-73. [PMID: 25261522 DOI: 10.1128/aem.02430-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species. Three putative VHPO genes were predicted in the genome of the flavobacterium Zobellia galactanivorans, a marine bacterium associated with macroalgae. In a phylogenetic analysis, these putative bacterial VHPO were closely related to other VHPO from diverse bacterial phyla but clustered independently from eukaryotic algal VBPO and fungal VCPO. Two of these bacterial VHPO, heterogeneously produced in Escherichia coli, were found to be strictly specific for iodide oxidation. The crystal structure of one of these vanadium-dependent iodoperoxidases, Zg-VIPO1, was solved by multiwavelength anomalous diffraction at 1.8 Å, revealing a monomeric structure mainly folded into α-helices. This three-dimensional structure is relatively similar to those of VCPO of the fungus Curvularia inaequalis and of Streptomyces sp. and is superimposable onto the dimeric structure of algal VBPO. Surprisingly, the vanadate binding site of Zg-VIPO1 is strictly conserved with the fungal VCPO active site. Using site-directed mutagenesis, we showed that specific amino acids and the associated hydrogen bonding network around the vanadate center are essential for the catalytic properties and also the iodide specificity of Zg-VIPO1. Altogether, phylogeny and structure-function data support the finding that iodoperoxidase activities evolved independently in bacterial and algal lineages, and this sheds light on the evolution of the VHPO enzyme family.
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Lacroix C, Querol-Audí J, Roche M, Franco D, Froeyen M, Guerra P, Terme T, Vanelle P, Verdaguer N, Neyts J, Leyssen P. A novel benzonitrile analogue inhibits rhinovirus replication. J Antimicrob Chemother 2014; 69:2723-32. [DOI: 10.1093/jac/dku200] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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38
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Sciara G, Clarke OB, Tomasek D, Kloss B, Tabuso S, Byfield R, Cohn R, Banerjee S, Rajashankar KR, Slavkovic V, Graziano JH, Shapiro L, Mancia F. Structural basis for catalysis in a CDP-alcohol phosphotransferase. Nat Commun 2014; 5:4068. [PMID: 24923293 PMCID: PMC4098843 DOI: 10.1038/ncomms5068] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/08/2014] [Indexed: 12/21/2022] Open
Abstract
The CDP-alcohol phosphotransferase (CDP-AP) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a CDP-linked donor to an alcohol acceptor. This is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalysed solely by CDP-APs. Here we report the 2.0 Å resolution crystal structure of a representative CDP-AP from Archaeoglobus fulgidus. The enzyme (AF2299) is a homodimer, with each protomer consisting of six transmembrane helices and an N-terminal cytosolic domain. A polar cavity within the membrane accommodates the active site, lined with the residues from an absolutely conserved CDP-AP signature motif (D(1)xxD(2)G(1)xxAR...G(2)xxxD(3)xxxD(4)). Structures in the apo, CMP-bound, CDP-bound and CDP-glycerol-bound states define functional roles for each of these eight conserved residues and allow us to propose a sequential, base-catalysed mechanism universal for CDP-APs, in which the fourth aspartate (D4) acts as the catalytic base.
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Affiliation(s)
- Giuliano Sciara
- 1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2]
| | - Oliver B Clarke
- 1] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA [2]
| | - David Tomasek
- 1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2]
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, USA
| | - Shantelle Tabuso
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, USA
| | - Rushelle Byfield
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Raphael Cohn
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Surajit Banerjee
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, Illinois 60439, USA
| | - Kanagalaghatta R Rajashankar
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, Illinois 60439, USA
| | - Vesna Slavkovic
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
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Identification of lysine residues in the Borrelia burgdorferi DbpA adhesin required for murine infection. Infect Immun 2014; 82:3186-98. [PMID: 24842928 DOI: 10.1128/iai.02036-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Decorin-binding protein A (DbpA) of Borrelia burgdorferi mediates bacterial adhesion to heparin and dermatan sulfate associated with decorin. Lysines K82, K163, and K170 of DbpA are known to be important for in vitro interaction with decorin, and the DbpA structure, initially solved by nuclear magnetic resonance (NMR) spectroscopy, suggests these lysine residues colocalize in a pocket near the C terminus of the protein. In the current study, we solved the structure of DbpA from B. burgdorferi strain 297 using X-ray crystallography and confirmed the existing NMR structural data. In vitro binding experiments confirmed that recombinant DbpA proteins with mutations in K82, K163, or K170 did not bind decorin, which was due to an inability to interact with dermatan sulfate. Most importantly, we determined that the in vitro binding defect observed upon mutation of K82, K163, or K170 in DbpA also led to a defect during infection. The infectivity of B. burgdorferi expressing individual dbpA lysine point mutants was assessed in mice challenged via needle inoculation. Murine infection studies showed that strains expressing dbpA with mutations in K82, K163, and K170 were significantly attenuated and could not be cultured from any tissue. Proper expression and cellular localization of the mutated DbpA proteins were examined, and NMR spectroscopy determined that the mutant DbpA proteins were structurally similar to wild-type DbpA. Taken together, these data showed that lysines K82, K163, and K170 potentiate the binding of DbpA to dermatan sulfate and that an interaction(s) mediated by these lysines is essential for B. burgdorferi murine infection.
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40
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Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Proc Natl Acad Sci U S A 2013; 110:20063-8. [PMID: 24277846 DOI: 10.1073/pnas.1312128110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.
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41
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Qian P, Papiz MZ, Jackson PJ, Brindley AA, Ng IW, Olsen JD, Dickman MJ, Bullough PA, Hunter CN. Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX. Biochemistry 2013; 52:7575-85. [DOI: 10.1021/bi4011946] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pu Qian
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Miroslav Z. Papiz
- Institute
of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Philip J. Jackson
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Amanda A. Brindley
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Irene W. Ng
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - John D. Olsen
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Mark J. Dickman
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Per A. Bullough
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
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42
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Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD. Attachment site recognition and regulation of directionality by the serine integrases. Nucleic Acids Res 2013; 41:8341-56. [PMID: 23821671 PMCID: PMC3783163 DOI: 10.1093/nar/gkt580] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between ‘attachment sites’ in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP × attB synaptic complexes to initiate recombination, and how attL × attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.
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Affiliation(s)
- Karen Rutherford
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
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Casañas A, Querol-Audí J, Guerra P, Pous J, Tanaka H, Tsukihara T, Verdaguer N, Fita I. New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1054-61. [PMID: 23695250 DOI: 10.1107/s0907444913004472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/14/2013] [Indexed: 01/27/2023]
Abstract
The vault particle, with a molecular weight of about 10 MDa, is the largest ribonucleoprotein that has been described. The X-ray structure of intact rat vault has been solved at a resolution of 3.5 Å [Tanaka et al. (2009), Science, 323, 384-388], showing an overall barrel-shaped architecture organized into two identical moieties, each consisting of 39 copies of the major vault protein (MVP). The model deposited in the PDB includes 39 MVP copies (half a vault) in the crystal asymmetric unit. A 2.1 Å resolution structure of the seven N-terminal repeats (R1-7) of MVP has also been determined [Querol-Audí et al. (2009), EMBO J. 28, 3450-3457], revealing important discrepancies with respect to the MVP models for repeats R1 and R2. Here, the re-refinement of the vault structure by incorporating the high-resolution information available for the R1-7 domains, using the deformable elastic network (DEN) approach and maintaining strict 39-fold noncrystallographic symmetry is reported. The new refinement indicates that at the resolution presently available the MVP shell can be described well as only one independent subunit organized with perfect D39 molecular symmetry. This refinement reveals that significant rearrangements occur in the N-terminus of MVP during the closing of the two vault halves and that the 39-fold symmetry breaks in the cap region. These results reflect the highly dynamic nature of the vault structure and represent a necessary step towards a better understanding of the biology and regulation of this particle.
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Affiliation(s)
- Arnau Casañas
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
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Crystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases. PLoS One 2013; 8:e56138. [PMID: 23457513 PMCID: PMC3573020 DOI: 10.1371/journal.pone.0056138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 01/05/2013] [Indexed: 11/19/2022] Open
Abstract
Background Ruminococcus flavefaciens is one of the predominant fiber-degrading bacteria found in the rumen of herbivores. Bioinformatic analysis of the recently sequenced genome indicated that this bacterium produces one of the most intricate cellulosome systems known to date. A distinct ORF, encoding for a multi-modular protein, RflaF_05439, was discovered during mining of the genome sequence. It is composed of two tandem modules of currently undefined function that share 45% identity and a C-terminal X-dockerin modular dyad. Gaining insight into the diversity, architecture and organization of different types of proteins in the cellulosome system is essential for broadening our understanding of a multi-enzyme complex, considered to be one of the most efficient systems for plant cell wall polysaccharide degradation in nature. Methodology/Principal Findings Following bioinformatic analysis, the second tandem module of RflaF_05439 was cloned and its selenium-labeled derivative was expressed and crystallized. The crystals belong to space group P21 with unit-cell parameters of a = 65.81, b = 60.61, c = 66.13 Å, β = 107.66° and contain two protein molecules in the asymmetric unit. The crystal structure was determined at 1.38-Å resolution by X-ray diffraction using the single-wavelength anomalous dispersion (SAD) method and was refined to Rfactor and Rfree of 0.127 and 0.152 respectively. The protein molecule mainly comprises a β-sheet flanked by short α-helixes, and a globular α-helical domain. The structure was found to be structurally similar to members of the NlpC/P60 superfamily of cysteine peptidases. Conclusions/Significance The 3D structure of the second repeat of the RflaF_05439 enabled us to propose a role for the currently undefined function of this protein. Its putative function as a cysteine peptidase is inferred from in silico structural homology studies. It is therefore apparent that cellulosomes integrate proteins with other functions in addition to the classic well-defined carbohydrate active enzymes.
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45
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Xu X, Chang BW, Mans BJ, Ribeiro JMC, Andersen JF. Structure and ligand-binding properties of the biogenic amine-binding protein from the saliva of a blood-feeding insect vector of Trypanosoma cruzi. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:105-13. [PMID: 23275168 PMCID: PMC3532134 DOI: 10.1107/s0907444912043326] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/18/2012] [Indexed: 11/10/2022]
Abstract
Proteins that bind small-molecule mediators of inflammation and hemostasis are essential for blood-feeding by arthropod vectors of infectious disease. In ticks and triatomine insects, the lipocalin protein family is greatly expanded and members have been shown to bind biogenic amines, eicosanoids and ADP. These compounds are potent mediators of platelet activation, inflammation and vascular tone. In this paper, the structure of the amine-binding protein (ABP) from Rhodnius prolixus, a vector of the trypanosome that causes Chagas disease, is described. ABP binds the biogenic amines serotonin and norepinephrine with high affinity. A complex with tryptamine shows the presence of a binding site for a single ligand molecule in the central cavity of the β-barrel structure. The cavity contains significant additional volume, suggesting that this protein may have evolved from the related nitrophorin proteins, which bind a much larger heme ligand in the central cavity.
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Affiliation(s)
- Xueqing Xu
- Laboratory of Malaria and Vector Research, NIH/NIAID, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
| | - Bianca W. Chang
- Laboratory of Malaria and Vector Research, NIH/NIAID, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
| | - Ben J. Mans
- Laboratory of Malaria and Vector Research, NIH/NIAID, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
- Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort 0110, South Africa
| | - Jose M. C. Ribeiro
- Laboratory of Malaria and Vector Research, NIH/NIAID, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
| | - John F. Andersen
- Laboratory of Malaria and Vector Research, NIH/NIAID, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
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Structure of alphacoronavirus transmissible gastroenteritis virus nsp1 has implications for coronavirus nsp1 function and evolution. J Virol 2012; 87:2949-55. [PMID: 23269811 DOI: 10.1128/jvi.03163-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Coronavirus nsp1 has been shown to induce suppression of host gene expression and to interfere with the host immune response. However, the mechanism is currently unknown. The only available structural information on coronavirus nsp1 is the nuclear magnetic resonance (NMR) structure of the N-terminal domain of nsp1 from severe acute respiratory syndrome coronavirus (SARS-CoV) from the betacoronavirus genus. Here we present the first nsp1 structure from an alphacoronavirus, transmissible gastroenteritis virus (TGEV) nsp1. It displays a six-stranded β-barrel fold with a long alpha helix on the rim of the barrel, a fold shared with SARS-CoV nsp1(13-128). Contrary to previous speculation, the TGEV nsp1 structure suggests that coronavirus nsp1s have a common origin, despite the lack of sequence homology. However, comparisons of surface electrostatics, shape, and amino acid conservation between the alpha- and betacoronaviruses lead us to speculate that the mechanism for nsp1-induced suppression of host gene expression might be different in these two genera.
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47
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Ragusa MJ, Stanley RE, Hurley JH. Architecture of the Atg17 complex as a scaffold for autophagosome biogenesis. Cell 2012; 151:1501-1512. [PMID: 23219485 DOI: 10.1016/j.cell.2012.11.028] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/09/2012] [Accepted: 10/30/2012] [Indexed: 10/27/2022]
Abstract
Macroautophagy is a bulk clearance mechanism in which the double-membraned phagophore grows and engulfs cytosolic material. In yeast, the phagophore nucleates from a cluster of 20-30 nm diameter Atg9-containing vesicles located at a multiprotein assembly known as the preautophagosomal structure (PAS). The crystal structure of a 2:2:2 complex of the earliest acting PAS proteins, Atg17, Atg29, and Atg31, was solved at 3.05 Å resolution. Atg17 is crescent shaped with a 10 nm radius of curvature. Dimerization of the Atg17-Atg31-Atg29 complex is critical for both PAS formation and autophagy, and each dimer contains two separate and complete crescents. Upon induction of autophagy, Atg17-Atg31-Atg29 assembles with Atg1 and Atg13, which in turn initiates the formation of the phagophore. The C-terminal EAT domain of Atg1 was shown to sense membrane curvature, dimerize, and tether lipid vesicles. These data suggest a structural mechanism for the organization of Atg9 vesicles into the early phagophore.
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Affiliation(s)
- Michael J Ragusa
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Robin E Stanley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - James H Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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Structure of the type III secretion effector protein ExoU in complex with its chaperone SpcU. PLoS One 2012; 7:e49388. [PMID: 23166655 PMCID: PMC3498133 DOI: 10.1371/journal.pone.0049388] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 10/10/2012] [Indexed: 11/21/2022] Open
Abstract
Disease causing bacteria often manipulate host cells in a way that facilitates the infectious process. Many pathogenic gram-negative bacteria accomplish this by using type III secretion systems. In these complex secretion pathways, bacterial chaperones direct effector proteins to a needle-like secretion apparatus, which then delivers the effector protein into the host cell cytosol. The effector protein ExoU and its chaperone SpcU are components of the Pseudomonas aeruginosa type III secretion system. Secretion of ExoU has been associated with more severe infections in both humans and animal models. Here we describe the 1.92 Å X-ray structure of the ExoU–SpcU complex, a full-length type III effector in complex with its full-length cognate chaperone. Our crystallographic data allow a better understanding of the mechanism by which ExoU kills host cells and provides a foundation for future studies aimed at designing inhibitors of this potent toxin.
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49
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Infantes L, Otero LH, Beassoni PR, Boetsch C, Lisa AT, Domenech CE, Albert A. The Structural Domains of Pseudomonas aeruginosa Phosphorylcholine Phosphatase Cooperate in Substrate Hydrolysis: 3D Structure and Enzymatic Mechanism. J Mol Biol 2012; 423:503-14. [DOI: 10.1016/j.jmb.2012.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/25/2012] [Accepted: 07/28/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Lourdes Infantes
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
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Jansen S, Perrakis A, Ulens C, Winkler C, Andries M, Joosten RP, Van Acker M, Luyten FP, Moolenaar WH, Bollen M. Structure of NPP1, an ectonucleotide pyrophosphatase/phosphodiesterase involved in tissue calcification. Structure 2012; 20:1948-59. [PMID: 23041369 DOI: 10.1016/j.str.2012.09.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 08/25/2012] [Accepted: 09/02/2012] [Indexed: 10/27/2022]
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase-1 (NPP1) converts extracellular nucleotides into inorganic pyrophosphate, whereas its close relative NPP2/autotaxin hydrolyzes lysophospholipids. NPP1 regulates calcification in mineralization-competent tissues, and a lack of NPP1 function underlies calcification disorders. Here, we show that NPP1 forms homodimers via intramembrane disulfide bonding, but is also processed intracellularly to a secreted monomer. The structure of secreted NPP1 reveals a characteristic bimetallic active site and a nucleotide-binding groove, but it lacks the lipid-binding pocket and open tunnel present in NPP2. A loop adjacent to the nucleotide-binding site, which is disordered in NPP2, is well ordered in NPP1 and might promote nucleotide binding. Remarkably, the N-terminal somatomedin B-like domains of NPP1, unlike those in NPP2, are flexible and do not contact the catalytic domain. Our results provide a structural basis for the nucleotide pyrophosphatase activity of NPP1 and help to understand how disease-causing mutations may affect NPP1 structure and function.
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Affiliation(s)
- Silvia Jansen
- Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
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