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Liu S, Li S, Yang Y, Li W. Termini restraining of small membrane proteins enables structure determination at near-atomic resolution. SCIENCE ADVANCES 2020; 6:6/51/eabe3717. [PMID: 33355146 DOI: 10.1126/sciadv.abe3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The termini-restrained proteins are functional and show improved stability during overexpression and purification. The reassembled GFP provides a versatile scaffold for membrane protein crystallization, enables diffraction to atomic resolution, and facilitates crystal identification, phase determination, and density modification. This strategy gives rise to 14 new structures of five vertebrate proteins from distinct functional families, bringing a substantial expansion to the structural database of small membrane proteins. Moreover, a high-resolution structure of bacterial DsbB reveals that this thiol oxidoreductase is activated through a catalytic triad, similar to cysteine proteases. Overall, termini restraining proves exceptionally effective for stabilization and structure determination of small membrane proteins.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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2
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Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes. J Mol Biol 2018; 430:4132-4141. [PMID: 30121295 DOI: 10.1016/j.jmb.2018.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022]
Abstract
We report the revised crystal structure of a pseudo-typed human adenovirus at 3.8-Å resolution that is consistent with the atomic models of minor proteins determined by cryo-electron microscopy. The diffraction data from multiple crystals were rescaled and merged to increase the data completeness. The densities for the minor proteins were initially identified in the phase-refined omit maps that were further improved by the phases from docked poly-alanine models to build atomic structures. While the trimeric fiber molecules are disordered due to flexibility and imposition of 5-fold symmetry, the remaining major capsid proteins hexon and penton base are clearly ordered, with the exception of hypervariable region 1 of hexons, the RGD containing loop, and the N-termini of the penton base. The exterior minor protein IX together with the interior minor proteins IIIa and VIII stabilizes the adenovirus virion. A segment of N-terminal pro-peptide of VI is found in the interior cavities of peripentonal hexons, and the rest of VI is disordered. While the triskelion substructures formed by the N-termini of IX conform to excellent quasi 3-fold symmetry, the tetrameric coiled-coils formed by the C-termini and organized in parallel and anti-parallel arrangement do not exhibit any quasi-symmetry. This observation also conveys the pitfalls of using the quasi-equivalence as validation criteria for the structural analysis of extended (non-modular) capsid proteins such as IX. Together, these results remedy certain discrepancies in the previous X-ray model in agreement with the cryo-electron microscopy models.
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3
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Virion Structure of Black Queen Cell Virus, a Common Honeybee Pathogen. J Virol 2017; 91:JVI.02100-16. [PMID: 28077635 PMCID: PMC5331821 DOI: 10.1128/jvi.02100-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/21/2016] [Indexed: 01/06/2023] Open
Abstract
Viral diseases are a major threat to honeybee (Apis mellifera) populations worldwide and therefore an important factor in reliable crop pollination and food security. Black queen cell virus (BQCV) is the etiological agent of a fatal disease of honeybee queen larvae and pupae. The virus belongs to the genus Triatovirus from the family Dicistroviridae, which is part of the order Picornavirales. Here we present a crystal structure of BQCV determined to a resolution of 3.4 Å. The virion is formed by 60 copies of each of the major capsid proteins VP1, VP2, and VP3; however, there is no density corresponding to a 75-residue-long minor capsid protein VP4 encoded by the BQCV genome. We show that the VP4 subunits are present in the crystallized virions that are infectious. This aspect of the BQCV virion is similar to that of the previously characterized triatoma virus and supports the recent establishment of the separate genus Triatovirus within the family Dicistroviridae. The C terminus of VP1 and CD loops of capsid proteins VP1 and VP3 of BQCV form 34-Å-tall finger-like protrusions at the virion surface. The protrusions are larger than those of related dicistroviruses. IMPORTANCE The western honeybee is the most important pollinator of all, and it is required to sustain the agricultural production and biodiversity of wild flowering plants. However, honeybee populations worldwide are suffering from virus infections that cause colony losses. One of the most common, and least known, honeybee pathogens is black queen cell virus (BQCV), which at high titers causes queen larvae and pupae to turn black and die. Here we present the three-dimensional virion structure of BQCV, determined by X-ray crystallography. The structure of BQCV reveals large protrusions on the virion surface. Capsid protein VP1 of BQCV does not contain a hydrophobic pocket. Therefore, the BQCV virion structure provides evidence that capsid-binding antiviral compounds that can prevent the replication of vertebrate picornaviruses may be ineffective against honeybee virus infections.
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Gai D, Wang D, Li SX, Chen XS. The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA. eLife 2016; 5. [PMID: 27921994 PMCID: PMC5140265 DOI: 10.7554/elife.18129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022] Open
Abstract
DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How these hexameric helicases interact with their origin dsDNA remains unknown. Here, we report the co-crystal structure of the SV40 Large-T Antigen (LT) hexameric helicase bound to its origin dsDNA. The structure shows that the six subunits form a near-planar ring that interacts with the origin, so that each subunit makes unique contacts with the DNA. The origin dsDNA inside the narrower AAA+ domain channel shows partial melting due to the compression of the two phosphate backbones, forcing Watson-Crick base-pairs within the duplex to flip outward. This structure provides the first snapshot of a hexameric helicase binding to origin dsDNA, and suggests a possible mechanism of origin melting by LT during SV40 replication in eukaryotic cells.
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Affiliation(s)
- Dahai Gai
- Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Program, University of Southern California, Los Angeles, United States
| | - Damian Wang
- Department of Biological Sciences, Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Shu-Xing Li
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, United States
| | - Xiaojiang S Chen
- Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Program, University of Southern California, Los Angeles, United States.,Department of Biological Sciences, Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, United States.,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, United States.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, United States
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5
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Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 2016; 540:80-85. [PMID: 27842381 DOI: 10.1038/nature20560] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/24/2016] [Indexed: 01/29/2023]
Abstract
In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNASec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNASec recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNASec binding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB-Sec-tRNASec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASec covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNASec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.
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Affiliation(s)
- Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Zhe Wang
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alena Paleskava
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrey L Konevega
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August University Göttingen, Justus-von Liebig Weg 11, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution. J Virol 2016; 90:7444-7455. [PMID: 27279610 PMCID: PMC4984619 DOI: 10.1128/jvi.00680-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 05/27/2016] [Indexed: 12/29/2022] Open
Abstract
The western honeybee (Apis mellifera) is the most important commercial insect pollinator. However, bees are under pressure from habitat loss, environmental stress, and pathogens, including viruses that can cause lethal epidemics. Slow bee paralysis virus (SBPV) belongs to the Iflaviridae family of nonenveloped single-stranded RNA viruses. Here we present the structure of the SBPV virion determined from two crystal forms to resolutions of 3.4 Å and 2.6 Å. The overall structure of the virion resembles that of picornaviruses, with the three major capsid proteins VP1 to 3 organized into a pseudo-T3 icosahedral capsid. However, the SBPV capsid protein VP3 contains a C-terminal globular domain that has not been observed in other viruses from the order Picornavirales. The protruding (P) domains form “crowns” on the virion surface around each 5-fold axis in one of the crystal forms. However, the P domains are shifted 36 Å toward the 3-fold axis in the other crystal form. Furthermore, the P domain contains the Ser-His-Asp triad within a surface patch of eight conserved residues that constitutes a putative catalytic or receptor-binding site. The movements of the domain might be required for efficient substrate cleavage or receptor binding during virus cell entry. In addition, capsid protein VP2 contains an RGD sequence that is exposed on the virion surface, indicating that integrins might be cellular receptors of SBPV.
IMPORTANCE Pollination by honeybees is needed to sustain agricultural productivity as well as the biodiversity of wild flora. However, honeybee populations in Europe and North America have been declining since the 1950s. Honeybee viruses from the Iflaviridae family are among the major causes of honeybee colony mortality. We determined the virion structure of an Iflavirus, slow bee paralysis virus (SBPV). SBPV exhibits unique structural features not observed in other picorna-like viruses. The SBPV capsid protein VP3 has a large C-terminal domain, five of which form highly prominent protruding “crowns” on the virion surface. However, the domains can change their positions depending on the conditions of the environment. The domain includes a putative catalytic or receptor binding site that might be important for SBPV cell entry.
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Yoshimura M, Chen NC, Guan HH, Chuankhayan P, Lin CC, Nakagawa A, Chen CJ. Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus. Acta Crystallogr D Struct Biol 2016; 72:830-40. [PMID: 27377380 PMCID: PMC4932916 DOI: 10.1107/s2059798316007695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 11/11/2022] Open
Abstract
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.
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Affiliation(s)
- Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
- Institute of Biotechnology and University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
- Institute of Biotechnology and University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu 39943, Taiwan
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8
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Structure of the host-recognition device of Staphylococcus aureus phage ϕ11. Sci Rep 2016; 6:27581. [PMID: 27282779 PMCID: PMC4901313 DOI: 10.1038/srep27581] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/17/2016] [Indexed: 12/16/2022] Open
Abstract
Phages play key roles in the pathogenicity and adaptation of the human pathogen Staphylococcus aureus. However, little is known about the molecular recognition events that mediate phage adsorption to the surface of S. aureus. The lysogenic siphophage ϕ11 infects S. aureus SA113. It was shown previously that ϕ11 requires α- or β-N-acetylglucosamine (GlcNAc) moieties on cell wall teichoic acid (WTA) for adsorption. Gp45 was identified as the receptor binding protein (RBP) involved in this process and GlcNAc residues on WTA were found to be the key component of the ϕ11 receptor. Here we report the crystal structure of the RBP of ϕ11, which assembles into a large, multidomain homotrimer. Each monomer contains a five-bladed propeller domain with a cavity that could accommodate a GlcNAc moiety. An electron microscopy reconstruction of the ϕ11 host adhesion component, the baseplate, reveals that six RBP trimers are assembled around the baseplate core. The Gp45 and baseplate structures provide insights into the overall organization and molecular recognition process of the phage ϕ11 tail. This assembly is conserved among most glycan-recognizing Siphoviridae, and the RBP orientation would allow host adhesion and infection without an activation step.
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Sabin C, Plevka P. The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning. Acta Crystallogr F Struct Biol Commun 2016; 72:188-97. [PMID: 26919522 PMCID: PMC4774877 DOI: 10.1107/s2053230x16000923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/15/2016] [Indexed: 01/08/2023] Open
Abstract
Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C(α) atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.
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Affiliation(s)
- Charles Sabin
- Central European Institute of Technology – Masaryk University, Kamenice 653/25, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology – Masaryk University, Kamenice 653/25, 625 00 Brno, Czech Republic
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The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid. J Virol 2015; 90:1377-86. [PMID: 26581987 PMCID: PMC4719609 DOI: 10.1128/jvi.02346-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/09/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Parechoviruses are human pathogens that cause diseases ranging from gastrointestinal disorders to encephalitis. Unlike those of most picornaviruses, parechovirus capsids are composed of only three subunits: VP0, VP1, and VP3. Here, we present the structure of a human parechovirus 1 (HPeV-1) virion determined to a resolution of 3.1 Å. We found that interactions among pentamers in the HPeV-1 capsid are mediated by the N termini of VP0s, which correspond to the capsid protein VP4 and the N-terminal part of the capsid protein VP2 of other picornaviruses. In order to facilitate delivery of the virus genome into the cytoplasm, the N termini of VP0s have to be released from contacts between pentamers and exposed at the particle surface, resulting in capsid disruption. A hydrophobic pocket, which can be targeted by capsid-binding antiviral compounds in many other picornaviruses, is not present in HPeV-1. However, we found that interactions between the HPeV-1 single-stranded RNA genome and subunits VP1 and VP3 in the virion impose a partial icosahedral ordering on the genome. The residues involved in RNA binding are conserved among all parechoviruses, suggesting a putative role of the genome in virion stability or assembly. Therefore, putative small molecules that could disrupt HPeV RNA-capsid protein interactions could be developed into antiviral inhibitors. IMPORTANCE Human parechoviruses (HPeVs) are pathogens that cause diseases ranging from respiratory and gastrointestinal disorders to encephalitis. Recently, there have been outbreaks of HPeV infections in Western Europe and North America. We present the first atomic structure of parechovirus HPeV-1 determined by X-ray crystallography. The structure explains why HPeVs cannot be targeted by antiviral compounds that are effective against other picornaviruses. Furthermore, we found that the interactions of the HPeV-1 genome with the capsid resulted in a partial icosahedral ordering of the genome. The residues involved in RNA binding are conserved among all parechoviruses, suggesting an evolutionarily fixed role of the genome in virion assembly. Therefore, putative small molecules disrupting HPeV RNA-capsid protein interactions could be developed into antiviral inhibitors.
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Sialic acid-dependent cell entry of human enterovirus D68. Nat Commun 2015; 6:8865. [PMID: 26563423 PMCID: PMC4660200 DOI: 10.1038/ncomms9865] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/09/2015] [Indexed: 01/30/2023] Open
Abstract
Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studies on the receptor-mediated EV-D68 entry into host cells. Here we demonstrate that cell surface sialic acid is essential for EV-D68 to bind to and infect susceptible cells. Crystal structures of EV-D68 in complex with sialylated glycan receptor analogues show that they bind into the ‘canyon' on the virus surface. The sialic acid receptor induces a cascade of conformational changes in the virus to eject a fatty-acid-like molecule that regulates the stability of the virus. Thus, virus binding to a sialic acid receptor and to immunoglobulin-like receptors used by most other enteroviruses share a conserved mechanism for priming viral uncoating and facilitating cell entry. The human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory infections, but despite its prevalence the exact mechanism mediating its cell entry have not been fully established. Here, the authors show how EV-D68 binds to sialic acid on the cell surface to initiate infection.
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12
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Chen NC, Yoshimura M, Guan HH, Wang TY, Misumi Y, Lin CC, Chuankhayan P, Nakagawa A, Chan SI, Tsukihara T, Chen TY, Chen CJ. Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection. PLoS Pathog 2015; 11:e1005203. [PMID: 26491970 PMCID: PMC4619592 DOI: 10.1371/journal.ppat.1005203] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/11/2015] [Indexed: 11/25/2022] Open
Abstract
Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis. The structure of a T = 3 Grouper nervous necrosis virus-like particle (GNNV-LP) is determined by the ab initio method with non-crystallographic symmetry averaging at 3.6 Å resolution. Each capsid protein (CP) shows three major domains: (i) the N-terminal arm, an inter-subunit extension at the inner surface; (ii) the shell domain (S-domain), a jelly-roll structure; and (iii) the protrusion domain (P-domain) formed by three-fold trimeric protrusions. In addition, we have determined structures of the T = 1 subviral particles (SVPs) of (i) the delta-P-domain mutant (residues 35−217) at 3.1 Å resolution; and (ii) the N-ARM deletion mutant (residues 35−338) at 7 Å resolution; and (iii) the structure of the individual P-domain (residues 214−338) at 1.2 Å resolution. The P-domain reveals a novel DxD motif asymmetrically coordinating two Ca2+ ions, and seems to play a prominent role in the calcium-mediated trimerization of the GNNV CPs during the initial capsid assembly process. The flexible N-ARM (N-terminal arginine-rich motif) appears to serve as a molecular switch for T = 1 or T = 3 assembly. Finally, we find that polyethylene glycol, which is incorporated into the P-domain during the crystallization process, enhances GNNV infection. The present structural studies together with the biological assays enhance our understanding of the role of the P-domain of GNNV in the capsid assembly and viral infection by this betanodavirus. Betanodaviruses belong to the family Nodaviridae and cause the mortality of numerous larval-stage fish species. Here we report protein crystal structures of a piscine betanodavirus, the Grouper nervous necrosis virus (GNNV), in four different forms. Highlights are two structural features that contribute to the viral molecular mechanisms of the T = 3 and T = 1 capsid assembly: a calcium-associated protrusion domain and a functional arginine-rich motif. These results also shed insights into the structural basis for evolutionary lineage of the family Nodaviridae.
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Affiliation(s)
- Nai-Chi Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Ting-Yu Wang
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Yuko Misumi
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Tomitake Tsukihara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan
| | - Tzong-Yueh Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (CJC)
| | - Chun-Jung Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan
- Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (CJC)
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13
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Abstract
The procedure for phase extension (PX) involves gradually extending the initial phases from low resolution (e.g., ~8Å) to the high-resolution limit of a diffraction data set. Structural redundancy present in the viral capsids that display icosahedral symmetry results in a high degree of non-crystallographic symmetry (NCS), which in turn translates into higher phasing power and is critical for improving and extending phases to higher resolution. Greater completeness of the diffraction data and determination of a molecular replacement solution, which entails accurately identifying the virus particle orientation(s) and position(s), are important for the smooth progression of the PX procedure. In addition, proper definition of a molecular mask (envelope) around the NCS-asymmetric unit has been found to be important for the success of density modification procedures, such as density averaging and solvent flattening. Regardless of the degree of NCS, the PX method appears to work well in all space groups, provided an accurate molecular mask is used along with reasonable initial phases. However, in the cases with space group P1, in addition to requiring a molecular mask, starting the phase extension at a higher resolution (e.g., 6Å) overcame the previously reported problems due to Babinet phases and phase flipping errors.
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Affiliation(s)
- Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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14
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Gill HS, Choi KY, Kammili L, Popratiloff A. Rescue of the temperature-sensitive, autosomal-recessive mutation R298S in the sodium-bicarbonate cotransporter NBCe1-A characterized by a weakened dimer and abnormal aggregation. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1850:1286-96. [PMID: 25743102 PMCID: PMC4424423 DOI: 10.1016/j.bbagen.2015.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/15/2015] [Accepted: 02/23/2015] [Indexed: 01/17/2023]
Abstract
BACKGROUND Band keratopathy, an ocular disease that is characterized by hypercalcemia and opaque bands across the cornea, has been associated with kidney disease. Type-II renal tubular acidosis (RTA), a condition in which the kidneys fail to recover bicarbonate (HCO3-) in the proximal tubule of the nephron, results in HCO3- wastage in the urine and low blood pH. The development of these diseases is associated with autosomal-recessive mutations in the Na+-coupled HCO3- cotransporter NBCe1-A located at the basolateral membranes of either cell type. METHODS We provide insight into the devastating R298S mutation found in type-II RTA-afflicted individuals using confocal-microscopy imaging of fluorescently-tagged NBCe1-A and NBCe1-A-R298S molecules expressed in human corneal endothelial and proximal tubule cells and from in-depth biophysical studies of their cytoplasmic N-terminal domains (Nt and Nt-R298S), including Nt crystal structure, melting-temperature, and homodimer dissociation constant (KD) analyses. RESULTS We illuminate and rescue trafficking defects of the R298S mutation of NBCe1-A. The KD for Nt monomer-dimer equilibrium is established. The KD for Nt-R298S is significantly higher, but immeasurable due to environmental factors (pH, temperature, concentration) that result in dimer instability leading to precipitation. The crystal structure of Nt-dimer shows that R298 is part of a putative substrate conduit and resides near the dimer interface held together by hydrogen-bond networks. CONCLUSIONS The R298S is a temperature-sensitive mutation in Nt that results in instability of the colloidal system leading to abnormal aggregation. GENERAL SIGNIFICANCE Our findings provide new perspectives to the aberrant mechanism of certain ocular pathologies and type-II RTA associated with the R298S mutation.
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Affiliation(s)
- Harindarpal S Gill
- Department of Medicine, The George Washington University; Division of Renal & Hypertension, The GW Medical Faculty Associates, 2300 I (eye) Street NW, Ross Hall Room 436B, Washington D.C. 20052, United States.
| | - Kun-Young Choi
- Department of Medicine, The George Washington University; Division of Renal & Hypertension, The GW Medical Faculty Associates, 2300 I (eye) Street NW, Ross Hall Room 436B, Washington D.C. 20052, United States
| | - Lakshmi Kammili
- Department of Medicine, The George Washington University; Division of Renal & Hypertension, The GW Medical Faculty Associates, 2300 I (eye) Street NW, Ross Hall Room 436B, Washington D.C. 20052, United States
| | - Anastas Popratiloff
- Department of Medicine, The George Washington University; Division of Renal & Hypertension, The GW Medical Faculty Associates, 2300 I (eye) Street NW, Ross Hall Room 436B, Washington D.C. 20052, United States
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15
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Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 2015; 520:567-70. [DOI: 10.1038/nature14275] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/30/2015] [Indexed: 12/18/2022]
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16
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Liu Y, Sheng J, Fokine A, Meng G, Shin WH, Long F, Kuhn RJ, Kihara D, Rossmann MG. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science 2015; 347:71-4. [PMID: 25554786 DOI: 10.1126/science.1261962] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks of respiratory illness in children in the United States. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid-binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug-binding pocket in viral protein 1 contained density that is consistent with a fatty acid of about 10 carbon atoms. This density could be displaced by pleconaril. We also showed that pleconaril inhibits EV-D68 at a half-maximal effective concentration of 430 nanomolar and might, therefore, be a possible drug candidate to alleviate EV-D68 outbreaks.
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Affiliation(s)
- Yue Liu
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Ju Sheng
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Andrei Fokine
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Geng Meng
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Woong-Hee Shin
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Feng Long
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA. Department of Computer Science, 305 North University Street, Purdue University, West Lafayette, IN 47907, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA.
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17
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Wang J. On the validation of crystallographic symmetry and the quality of structures. Protein Sci 2014; 24:621-32. [PMID: 25352397 DOI: 10.1002/pro.2595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 11/06/2022]
Abstract
In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the "pseudosymmetry" and "special NCS" that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as Rfree that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as "special NCS" or "pseudosymmetry". When mistakes of this kind are made, artificially low values of Rfree can give unjustified confidence in the accuracy of the reported structures.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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18
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Yap ML, Klose T, Plevka P, Aksyuk A, Zhang X, Arisaka F, Rossmann MG. Structure of the 3.3MDa, in vitro assembled, hubless bacteriophage T4 baseplate. J Struct Biol 2014; 187:95-102. [PMID: 24998893 PMCID: PMC4130566 DOI: 10.1016/j.jsb.2014.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/16/2014] [Accepted: 06/25/2014] [Indexed: 01/07/2023]
Abstract
The bacteriophage T4 baseplate is the control center of the virus, where the recognition of an Escherichiacoli host by the long tail fibers is translated into a signal to initiate infection. The short tail fibers unfold from the baseplate for firm attachment to the host, followed by shrinkage of the tail sheath that causes the tail tube to enter and cross the periplasmic space ending with injection of the genome into the host. During this process, the 6.5MDa baseplate changes its structure from a "dome" shape to a "star" shape. An in vitro assembled hubless baseplate has been crystallized. It consists of six copies of the recombinantly expressed trimeric gene product (gp) 10, monomeric gp7, dimeric gp8, dimeric gp6 and monomeric gp53. The diffraction pattern extends, at most, to 4.0Å resolution. The known partial structures of gp10, gp8, and gp6 and their relative position in the baseplate derived from earlier electron microscopy studies were used for molecular replacement. An electron density map has been calculated based on molecular replacement, single isomorphous replacement with anomalous dispersion data and 2-fold non-crystallographic symmetry averaging between two baseplate wedges in the crystallographic asymmetric unit. The current electron density map indicates that there are structural changes in the gp6, gp8, and gp10 oligomers compared to their structures when separately crystallized. Additional density is also visible corresponding to gp7, gp53 and the unknown parts of gp10 and gp6.
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Affiliation(s)
- Moh Lan Yap
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
| | - Pavel Plevka
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
| | - Anastasia Aksyuk
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
| | - Xinzheng Zhang
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
| | - Fumio Arisaka
- Department of Life Science, Tokyo Institute of Technology, 4259 Midori-ku, Nagatsuta, Yokohama 226-8501, Japan
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA,Corresponding author at: Purdue University, Department of Biological Sciences, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA. Fax: (765) 496-1189. Telephone: (765) 494-4911. (M. Rossmann)
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19
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Wang J, Wing RA. Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data. ACTA ACUST UNITED AC 2014; 70:1491-7. [PMID: 24816117 DOI: 10.1107/s1399004714005318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/07/2014] [Indexed: 11/11/2022]
Abstract
Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Richard A Wing
- Laboratory of Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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20
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Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ϕ6 Major Capsid Protein. Protein J 2013; 32:635-40. [DOI: 10.1007/s10930-013-9526-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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The structure of the KtrAB potassium transporter. Nature 2013; 496:323-8. [PMID: 23598340 DOI: 10.1038/nature12055] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 03/05/2013] [Indexed: 12/23/2022]
Abstract
In bacteria, archaea, fungi and plants the Trk, Ktr and HKT ion transporters are key components of osmotic regulation, pH homeostasis and resistance to drought and high salinity. These ion transporters are functionally diverse: they can function as Na(+) or K(+) channels and possibly as cation/K(+) symporters. They are closely related to potassium channels both at the level of the membrane protein and at the level of the cytosolic regulatory domains. Here we describe the crystal structure of a Ktr K(+) transporter, the KtrAB complex from Bacillus subtilis. The structure shows the dimeric membrane protein KtrB assembled with a cytosolic octameric KtrA ring bound to ATP, an activating ligand. A comparison between the structure of KtrAB-ATP and the structures of the isolated full-length KtrA protein with ATP or ADP reveals a ligand-dependent conformational change in the octameric ring, raising new ideas about the mechanism of activation in these transporters.
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22
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Makino DL, Larson SB, McPherson A. The crystallographic structure of Panicum Mosaic Virus (PMV). J Struct Biol 2013; 181:37-52. [PMID: 23123270 PMCID: PMC3525795 DOI: 10.1016/j.jsb.2012.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/25/2012] [Accepted: 10/01/2012] [Indexed: 11/21/2022]
Abstract
The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.
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Affiliation(s)
- Debora L. Makino
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697-3900
| | - Steven B. Larson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697-3900
| | - Alexander McPherson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697-3900
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23
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Zeng Y, Larson SB, Heitsch CE, McPherson A, Harvey SC. A model for the structure of satellite tobacco mosaic virus. J Struct Biol 2012; 180:110-6. [PMID: 22750417 DOI: 10.1016/j.jsb.2012.06.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/08/2012] [Accepted: 06/14/2012] [Indexed: 11/24/2022]
Abstract
Satellite tobacco mosaic virus (STMV) is an icosahedral T=1 single-stranded RNA virus with a genome containing 1058 nucleotides. X-ray crystallography revealed a structure containing 30 double-helical RNA segments, with each helix having nine base pairs and an unpaired nucleotide at the 3' end of each strand. Based on this structure, Larson and McPherson proposed a model of 30 hairpin-loop elements occupying the edges of the icosahedron and connected by single-stranded regions. More recently, Schroeder et al. have combined the results of chemical probing with a novel helix searching algorithm to propose a specific secondary structure for the STMV genome, compatible with the Larson-McPherson model. Here we report an all-atom model of STMV, using the complete protein and RNA sequences and the Schroeder RNA secondary structure. As far as we know, this is the first all-atom model for the complete structure of any virus (100% of the atoms) using the natural genomic sequence.
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Affiliation(s)
- Yingying Zeng
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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24
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Aksyuk AA, Kurochkina LP, Fokine A, Forouhar F, Mesyanzhinov VV, Tong L, Rossmann MG. Structural conservation of the myoviridae phage tail sheath protein fold. Structure 2011; 19:1885-94. [PMID: 22153511 PMCID: PMC3256926 DOI: 10.1016/j.str.2011.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/22/2011] [Accepted: 09/12/2011] [Indexed: 01/07/2023]
Abstract
Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.
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Affiliation(s)
- Anastasia A. Aksyuk
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, U.S.A
| | - Lidia P. Kurochkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, Russia, 117997
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, U.S.A
| | - Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
| | - Vadim V. Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, Russia, 117997
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, U.S.A.,Correspondence: ; telephone (765) 494-4911; FAX (765) 496-1189
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25
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Pickens LB, Sawaya MR, Rasool H, Pashkov I, Yeates TO, Tang Y. Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. J Biol Chem 2011; 286:41539-41551. [PMID: 21965680 PMCID: PMC3308865 DOI: 10.1074/jbc.m111.299859] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/28/2011] [Indexed: 11/06/2022] Open
Abstract
SsfX3 is a GDSL family acyltransferase that transfers salicylate to the C-4 hydroxyl of a tetracycline intermediate in the penultimate step during biosynthesis of the anticancer natural product SF2575. The C-4 salicylate takes the place of the more common C-4 dimethylamine functionality, making SsfX3 the first acyltransferase identified to act on a tetracycline substrate. The crystal structure of SsfX3 was determined at 2.5 Å, revealing two distinct domains as follows: an N-terminal β-sandwich domain that resembles a carbohydrate-binding module, and a C-terminal catalytic domain that contains the atypical α/β-hydrolase fold found in the GDSL hydrolase family of enzymes. The active site lies at one end of a large open binding pocket, which is spatially defined by structural elements from both the N- and C-terminal domains. Mutational analysis in the putative substrate binding pocket identified residues from both domains that are important for binding the acyl donor and acceptor. Furthermore, removal of the N-terminal carbohydrate-binding module-like domain rendered the stand-alone α/β-hydrolase domain inactive. The additional noncatalytic module is therefore proposed to be required to define the binding pocket and provide sufficient interactions with the spatially extended tetracyclic substrate. SsfX3 was also demonstrated to accept a variety of non-native acyl groups. This relaxed substrate specificity toward the acyl donor allowed the chemoenzymatic biosynthesis of C-4-modified analogs of the immediate precursor to the bioactive SF2575; these were used to assay the structure activity relationships at the C-4 position.
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Affiliation(s)
- Lauren B Pickens
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Howard Hughes Medical Institute, and UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Huma Rasool
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095
| | - Inna Pashkov
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095
| | - Todd O Yeates
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Molecular Biology Institute, Los Angeles, California 90095
| | - Yi Tang
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095; Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Molecular Biology Institute, Los Angeles, California 90095.
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26
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Baumann BAJ, Taylor DW, Huang Z, Tama F, Fagnant PM, Trybus KM, Taylor KA. Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation. J Mol Biol 2011; 415:274-87. [PMID: 22079364 DOI: 10.1016/j.jmb.2011.10.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 10/22/2011] [Accepted: 10/27/2011] [Indexed: 11/26/2022]
Abstract
Smooth muscle myosin and smooth muscle heavy meromyosin (smHMM) are activated by regulatory light chain phosphorylation, but the mechanism remains unclear. Dephosphorylated, inactive smHMM assumes a closed conformation with asymmetric intramolecular head-head interactions between motor domains. The "free head" can bind to actin, but the actin binding interface of the "blocked head" is involved in interactions with the free head. We report here a three-dimensional structure for phosphorylated, active smHMM obtained using electron crystallography of two-dimensional arrays. Head-head interactions of phosphorylated smHMM resemble those found in the dephosphorylated state but occur between different molecules, not within the same molecule. The light chain binding domain structure of phosphorylated smHMM differs markedly from that of the "blocked" head of dephosphorylated smHMM. We hypothesize that regulatory light chain phosphorylation opens the inhibited conformation primarily by its effect on the blocked head. Singly phosphorylated smHMM is not compatible with the closed conformation if the blocked head is phosphorylated. This concept has implications for the extent of myosin activation at low levels of phosphorylation in smooth muscle.
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Affiliation(s)
- Bruce A J Baumann
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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27
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Yu S, Vit A, Devenish S, Mahanty HK, Itzen A, Goody RS, Blankenfeldt W. Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria. BMC STRUCTURAL BIOLOGY 2011; 11:33. [PMID: 21849072 PMCID: PMC3175449 DOI: 10.1186/1472-6807-11-33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 08/17/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND The phenazines are redox-active secondary metabolites that a large number of bacterial strains produce and excrete into the environment. They possess antibiotic activity owing to the fact that they can reduce molecular oxygen to toxic reactive oxygen species. In order to take advantage of this activity, phenazine producers need to protect themselves against phenazine toxicity. Whereas it is believed that phenazine-producing pseudomonads possess highly active superoxide dismutases and catalases, it has recently been found that the plant-colonizing bacterium Enterobacter agglomerans expresses a small gene ehpR to render itself resistant towards D-alanyl-griseoluteic acid, the phenazine antibiotic produced by this strain. RESULTS To understand the resistance mechanism installed by EhpR we have determined its crystal structure in the apo form at 2.15 Å resolution and in complex with griseoluteic acid at 1.01 Å, respectively. While EhpR shares a common fold with glyoxalase-I/bleomycin resistance proteins, the ligand binding site does not contain residues that some related proteins employ to chemically alter their substrates. Binding of the antibiotic is mediated by π-stacking interactions of the aromatic moiety with the side chains of aromatic amino acids and by a few polar interactions. The dissociation constant KD between EhpR and griseoluteic acid was quantified as 244 ± 45 μM by microscale thermophoresis measurements. CONCLUSIONS The data accumulated here suggest that EhpR confers resistance by binding D-alanyl-griseoluteic acid and acting as a chaperone involved in exporting the antibiotic rather than by altering it chemically. It is tempting to speculate that EhpR acts in concert with EhpJ, a transport protein of the major facilitator superfamily that is also encoded in the phenazine biosynthesis operon of E. agglomerans. The low affinity of EhpR for griseoluteic acid may be required for its physiological function.
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Affiliation(s)
- Shen Yu
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
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28
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Li W, Li F. Cross-crystal averaging with search models to improve molecular replacement phases. Structure 2011; 19:155-61. [PMID: 21300285 PMCID: PMC3037595 DOI: 10.1016/j.str.2010.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/29/2010] [Accepted: 12/13/2010] [Indexed: 11/25/2022]
Abstract
The application of molecular replacement (MR) in macromolecular crystallography can be limited by the “model bias” problem. Here we propose a strategy to reduce model bias when only part of a new structure is known: after the MR search, structure determination of the unknown part of the new structure can be facilitated by cross-crystal averaging of the known part of the new structure with the search model. This strategy dramatically improves electron density in the unknown part of the new structure. It has enabled us to determine the structures of two coronavirus receptor-binding domains each complexed with their receptor at moderate resolutions. In a test case, it also enabled automated model building when >50% of an antigen-antibody complex was absent. These results suggest that this averaging strategy can be routinely used after MR to enhance the interpretability of electron density associated with missing model.
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Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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29
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Structural insights into viral determinants of nematode mediated Grapevine fanleaf virus transmission. PLoS Pathog 2011; 7:e1002034. [PMID: 21625570 PMCID: PMC3098200 DOI: 10.1371/journal.ppat.1002034] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/16/2011] [Indexed: 11/19/2022] Open
Abstract
Many animal and plant viruses rely on vectors for their transmission from host to
host. Grapevine fanleaf virus (GFLV), a picorna-like virus from
plants, is transmitted specifically by the ectoparasitic nematode
Xiphinema index. The icosahedral capsid of GFLV, which
consists of 60 identical coat protein subunits (CP), carries the determinants of
this specificity. Here, we provide novel insight into GFLV transmission by
nematodes through a comparative structural and functional analysis of two GFLV
variants. We isolated a mutant GFLV strain (GFLV-TD) poorly transmissible by
nematodes, and showed that the transmission defect is due to a glycine to
aspartate mutation at position 297 (Gly297Asp) in the CP. We next determined the
crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of
GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed
loop at the outer surface of the capsid and did not affect the conformation of
the assembled capsid, nor of individual CP molecules. The loop is part of a
positively charged pocket that includes a previously identified determinant of
transmission. We propose that this pocket is a ligand-binding site with
essential function in GFLV transmission by X. index. Our data
suggest that perturbation of the electrostatic landscape of this pocket affects
the interaction of the virion with specific receptors of the nematode's
feeding apparatus, and thereby severely diminishes its transmission efficiency.
These data provide a first structural insight into the interactions between a
plant virus and a nematode vector. Numerous pathogenic viruses from animals and plants rely on vectors such as
insects, worms or other organisms for their transmission from host to host. The
reasons why certain vectors transmit some viruses but not others remain poorly
understood. In plants, Grapevine fanleaf virus (GFLV), a major
pathogen of grapes worldwide and its specific vector, the dagger nematode
Xiphinema index, provides a well-established model
illustrating this specificity. Here, we determined the high-resolution
structures of two GFLV isolates that differ in their transmissibility. We show
that this difference is due to a single mutation in a region exposed at the
outer surface of the viral particles. This mutation does not alter the
conformation of the particles but modifies the distribution of charges within a
positively-charged pocket at the outer surface of virions which likely affects
particle retention by X. index and, thereby also transmission
efficiency. Therefore, we propose that this pocket is involved in the specific
recognition of GFLV by its nematode vector. This work paves the way towards the
characterization of the specific compound(s) within the nematodes that trigger
vector specificity and provides novel perspectives to interfere with virus
transmission.
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30
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King-Scott J, Konarev PV, Panjikar S, Jordanova R, Svergun DI, Tucker PA. Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis. Structure 2011; 19:56-69. [PMID: 21220116 DOI: 10.1016/j.str.2010.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 01/29/2023]
Abstract
The open reading frame rv1364c of Mycobacterium tuberculosis, which regulates the stress-dependent σ factor, σ(F), has been analyzed structurally and functionally. Rv1364c contains domains with sequence similarity to the RsbP/RsbW/RsbV regulatory system of the stress-response σ factor of Bacillus subtilis. Rv1364c contains, sequentially, a PAS domain (which shows sequence similarity to the PAS domain of the B. subtilis RsbP protein), an active phosphatase domain, a kinase (anti-σ(F) like) domain and a C-terminal anti-σ(F) antagonist like domain. The crystal structures of two PAS domain constructs (at 2.3 and 1.6 Å) and a phosphatase/kinase dual domain construct (at 2.6 Å) are described. The PAS domain is shown to bind palmitic acid but to have 100 times greater affinity for palmitoleic acid. The full-length protein can exist in solution as both monomer and dimer. We speculate that a switch between monomer and dimer, possibly resulting from fatty acid binding, affects the accessibility of the serine of the C-terminal, anti-σ(F) antagonist domain for dephosphorylation by the phosphatase domain thus indirectly altering the availability of σ(F).
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Affiliation(s)
- Jack King-Scott
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D22603, Hamburg, Germany
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31
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Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli. J Bacteriol 2010; 192:6056-63. [PMID: 20851901 DOI: 10.1128/jb.00652-10] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The ethanolamine-utilizing bacterial microcompartment (Eut-BMC) of Escherichia coli is a polyhedral organelle that harbors specific enzymes for the catabolic degradation of ethanolamine. The compartment is composed of a proteinaceous shell structure that maintains a highly specialized environment for the biochemical reactions inside. Recent structural investigations have revealed hexagonal assemblies of shell proteins that form a tightly packed two-dimensional lattice that is likely to function as a selectively permeable protein membrane, wherein small channels are thought to permit controlled exchange of specific solutes. Here, we show with two nonisomorphous crystal structures that EutM also forms a two-dimensional protein membrane. As its architecture is highly similar to the membrane structure of EutL, it is likely that the structure represents a physiologically relevant form. Thus far, of all Eut proteins, only EutM and EutL have been shown to form such proteinaceous membranes. Despite their similar architectures, however, both proteins exhibit dramatically different pore structures. In contrast to EutL, the pore of EutM appears to be positively charged, indicating specificity for different solutes. Furthermore, we also show that the central pore structure of the EutL shell protein can be triggered to open specifically upon exposure to zinc ions, suggesting a specific gating mechanism.
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32
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Churchill MEA, Klass J, Zoetewey DL. Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending. J Mol Biol 2010; 403:88-102. [PMID: 20800069 DOI: 10.1016/j.jmb.2010.08.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/03/2010] [Accepted: 08/16/2010] [Indexed: 10/19/2022]
Abstract
The ubiquitous, eukaryotic, high-mobility group box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor-groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity, and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and 50 bp of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1 box A-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending.
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Affiliation(s)
- Mair E A Churchill
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Janet Klass
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - David L Zoetewey
- Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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Trapani S, Schoehn G, Navaza J, Abergel C. Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:514-21. [PMID: 20445226 DOI: 10.1107/s0907444910002763] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 01/22/2010] [Indexed: 11/10/2022]
Abstract
The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.
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34
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Galkin A, Kulakova L, Wu R, Nash TE, Dunaway-Mariano D, Herzberg O. X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:386-90. [PMID: 20383005 PMCID: PMC2852327 DOI: 10.1107/s1744309110004665] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 02/05/2010] [Indexed: 11/10/2022]
Abstract
Carbamate kinase catalyzes the reversible conversion of carbamoyl phosphate and ADP to ATP and ammonium carbamate, which is hydrolyzed to ammonia and carbonate. The three-dimensional structure of carbamate kinase from the human parasite Giardia lamblia (glCK) has been determined at 3 A resolution. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 69.77, b = 85.41, c = 102.1 A, beta = 106.8 degrees . The structure was refined to a final R factor of 0.227. The essentiality of glCK together with its absence in humans makes the enzyme an attractive candidate for anti-Giardia drug development. Steady-state kinetic rate constants have been determined. The k(cat) for ATP formation is 319 +/- 9 s(-1). The K(m) values for carbamoyl phosphate and ADP are 85 +/- 6 and 70 +/- 5 microM, respectively. The structure suggests that three invariant lysine residues (Lys131, Lys216 and Lys278) may be involved in the binding of substrates and phosphoryl transfer. The structure of glCK reveals that a glycerol molecule binds in the likely carbamoyl phosphate-binding site.
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Affiliation(s)
- Andrey Galkin
- W. M. Keck Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
| | - Liudmila Kulakova
- W. M. Keck Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
| | - Rui Wu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Theodore E. Nash
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Osnat Herzberg
- W. M. Keck Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
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35
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Conformational changes in the capsid of a calicivirus upon interaction with its functional receptor. J Virol 2010; 84:5550-64. [PMID: 20357100 DOI: 10.1128/jvi.02371-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonenveloped viral capsids are metastable structures that undergo conformational changes during virus entry that lead to interactions of the capsid or capsid fragments with the cell membrane. For members of the Caliciviridae, neither the nature of these structural changes in the capsid nor the factor(s) responsible for inducing these changes is known. Feline junctional adhesion molecule A (fJAM-A) mediates the attachment and infectious viral entry of feline calicivirus (FCV). Here, we show that the infectivity of some FCV isolates is neutralized following incubation with the soluble receptor at 37 degrees C. We used this property to select mutants resistant to preincubation with the soluble receptor. We isolated and sequenced 24 soluble receptor-resistant (srr) mutants and characterized the growth properties and receptor-binding activities of eight mutants. The location of the mutations within the capsid structure of FCV was mapped using a new 3.6-A structure of native FCV. The srr mutations mapped to the surface of the P2 domain were buried at the protruding domain dimer interface or were present in inaccessible regions of the capsid protein. Coupled with data showing that both the parental FCV and the srr mutants underwent increases in hydrophobicity upon incubation with the soluble receptor at 37 degrees C, these findings indicate that FCV likely undergoes conformational change upon interaction with its receptor. Changes in FCV capsid conformation following its interaction with fJAM-A may be important for subsequent interactions of the capsid with cellular membranes, membrane penetration, and genome delivery.
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36
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Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, Waksman G. Structure of the outer membrane complex of a type IV secretion system. Nature 2009; 462:1011-5. [PMID: 19946264 PMCID: PMC2797999 DOI: 10.1038/nature08588] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 10/19/2009] [Indexed: 02/07/2023]
Abstract
Type IV secretion systems are secretion nanomachines spanning the two membranes of Gram-negative bacteria. Three proteins, VirB7, VirB9 and VirB10, assemble into a 1.05 megadalton (MDa) core spanning the inner and outer membranes. This core consists of 14 copies of each of the proteins and forms two layers, the I and O layers, inserting in the inner and outer membrane, respectively. Here we present the crystal structure of a approximately 0.6 MDa outer-membrane complex containing the entire O layer. This structure is the largest determined for an outer-membrane channel and is unprecedented in being composed of three proteins. Unexpectedly, this structure identifies VirB10 as the outer-membrane channel with a unique hydrophobic double-helical transmembrane region. This structure establishes VirB10 as the only known protein crossing both membranes of Gram-negative bacteria. Comparison of the cryo-electron microscopy (cryo-EM) and crystallographic structures points to conformational changes regulating channel opening and closing.
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Affiliation(s)
- Vidya Chandran
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Rémi Fronzes
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Stéphane Duquerroy
- Institut Pasteur, Unité de Virologie Structurale, Virology Department and CNRS URA 3015, Paris, France
| | - Nora Cronin
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Jorge Navaza
- Laboratoire de Microscopie Electronique, Institut de Biologie Structurale J.P. Ebel, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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37
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Galkin A, Kulakova L, Wu R, Gong M, Dunaway-Mariano D, Herzberg O. X-ray structure and kinetic properties of ornithine transcarbamoylase from the human parasite Giardia lamblia. Proteins 2009; 76:1049-53. [PMID: 19507245 DOI: 10.1002/prot.22469] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrey Galkin
- W.M. Keck Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
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38
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Zimmer J, Rapoport TA. Conformational flexibility and peptide interaction of the translocation ATPase SecA. J Mol Biol 2009; 394:606-12. [PMID: 19850053 PMCID: PMC2832196 DOI: 10.1016/j.jmb.2009.10.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/08/2009] [Accepted: 10/09/2009] [Indexed: 11/26/2022]
Abstract
The SecA ATPase forms a functional complex with the protein-conducting SecY channel to translocate polypeptides across the bacterial cell membrane. SecA recognizes the translocation substrate and catalyzes its unidirectional movement through the SecY channel. The recent crystal structure of the Thermotoga maritima SecA-SecYEG complex shows the ATPase in a conformation where the nucleotide-binding domains (NBDs) have closed around a bound ADP-BeFx complex and SecA's polypeptide-binding clamp is shut. Here, we present the crystal structure of T. maritima SecA in isolation, determined in its ADP-bound form at 3.1 A resolution. SecA alone has a drastically different conformation in which the nucleotide-binding pocket between NBD1 and NBD2 is open and the preprotein cross-linking domain has rotated away from both NBDs, thereby opening the polypeptide-binding clamp. To investigate how this clamp binds polypeptide substrates, we also determined a structure of Bacillus subtilis SecA in complex with a peptide at 2.5 A resolution. This structure shows that the peptide augments the highly conserved beta-sheet at the back of the clamp. Taken together, these structures suggest a mechanism by which ATP hydrolysis can lead to polypeptide translocation.
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Affiliation(s)
- Jochen Zimmer
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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39
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The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly. J Mol Biol 2009; 391:635-47. [PMID: 19559027 DOI: 10.1016/j.jmb.2009.06.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/29/2009] [Accepted: 06/17/2009] [Indexed: 11/20/2022]
Abstract
The structure of the Leviviridae bacteriophage phiCb5 virus-like particle has been determined at 2.9 A resolution and the structure of the native bacteriophage phiCb5 at 3.6 A. The structures of the coat protein shell appear to be identical, while differences are found in the organization of the density corresponding to the RNA. The capsid is built of coat protein dimers and in shape corresponds to a truncated icosahedron with T = 3 quasi-symmetry. The capsid is stabilized by four calcium ions per icosahedral asymmetric unit. One is located at the symmetry axis relating the quasi-3-fold related subunits and is part of an elaborate network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilize the contacts within the coat protein dimer. The stability of the phiCb5 particles decreases when calcium ions are chelated with EDTA. In contrast to other leviviruses, phiCb5 particles are destabilized in solution with elevated salt concentration. The model of the phiCb5 capsid provides an explanation of the salt-induced destabilization of phiCb5, since hydrogen bonds, salt bridges and calcium ions have important roles in the intersubunit interactions. Electron density of three putative RNA nucleotides per icosahedral asymmetric unit has been observed in the phiCb5 structure. The nucleotides mediate contacts between the two subunits forming a dimer and a third subunit in another dimer. We suggest a model for phiCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The phiCb5 structure is the first example in the levivirus family that provides insight into the mechanism by which the genome-coat protein interaction may accelerate the capsid assembly and increase capsid stability.
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40
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Aksyuk AA, Leiman PG, Shneider MM, Mesyanzhinov VV, Rossmann MG. The Structure of Gene Product 6 of Bacteriophage T4, the Hinge-Pin of the Baseplate. Structure 2009; 17:800-8. [DOI: 10.1016/j.str.2009.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 04/11/2009] [Indexed: 10/20/2022]
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41
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Olea C, Boon EM, Pellicena P, Kuriyan J, Marletta MA. Probing the function of heme distortion in the H-NOX family. ACS Chem Biol 2008; 3:703-10. [PMID: 19032091 DOI: 10.1021/cb800185h] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoproteins carry out diverse functions utilizing a wide range of chemical reactivity while employing the same heme prosthetic group. It is clear from high-resolution crystal structures and biochemical studies that protein-bound hemes are not planar and adopt diverse conformations. The crystal structure of an H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) contains the most distorted heme reported to date. In this study, Tt H-NOX was engineered to adopt a flatter heme by mutating proline 115, a conserved residue in the H-NOX family, to alanine. Decreasing heme distortion in Tt H-NOX increases affinity for oxygen and decreases the reduction potential of the heme iron. Additionally, flattening the heme is associated with significant shifts in the N-terminus of the protein. These results show a clear link between the heme conformation and Tt H-NOX structure and demonstrate that heme distortion is an important determinant for maintaining biochemical properties in H-NOX proteins.
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Affiliation(s)
| | - Elizabeth M. Boon
- Department of Chemistry, California Institute for Quantitative Biosciences
| | | | - John Kuriyan
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael A. Marletta
- Department of Molecular and Cell Biology
- Department of Chemistry, California Institute for Quantitative Biosciences
- Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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42
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Yan X, Yu Z, Zhang P, Battisti AJ, Holdaway HA, Chipman PR, Bajaj C, Bergoin M, Rossmann MG, Baker TS. The capsid proteins of a large, icosahedral dsDNA virus. J Mol Biol 2008; 385:1287-99. [PMID: 19027752 DOI: 10.1016/j.jmb.2008.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/30/2008] [Accepted: 11/03/2008] [Indexed: 12/23/2022]
Abstract
Chilo iridescent virus (CIV) is a large (approximately 1850 A diameter) insect virus with an icosahedral, T=147 capsid, a double-stranded DNA (dsDNA) genome, and an internal lipid membrane. The structure of CIV was determined to 13 A resolution by means of cryoelectron microscopy (cryoEM) and three-dimensional image reconstruction. A homology model of P50, the CIV major capsid protein (MCP), was built based on its amino acid sequence and the structure of the homologous Paramecium bursaria chlorella virus 1 Vp54 MCP. This model was fitted into the cryoEM density for each of the 25 trimeric CIV capsomers per icosahedral asymmetric unit. A difference map, in which the fitted CIV MCP capsomers were subtracted from the CIV cryoEM reconstruction, showed that there are at least three different types of minor capsid proteins associated with the capsomers outside the lipid membrane. "Finger" proteins are situated at many, but not all, of the spaces between three adjacent capsomers within each trisymmetron, and "zip" proteins are situated between sets of three adjacent capsomers at the boundary between neighboring trisymmetrons and pentasymmetrons. Based on the results of segmentation and density correlations, there are at least eight finger proteins and three dimeric and two monomeric zip proteins in one asymmetric unit of the CIV capsid. These minor proteins appear to stabilize the virus by acting as intercapsomer cross-links. One transmembrane "anchor" protein per icosahedral asymmetric unit, which extends from beneath one of the capsomers in the pentasymmetron to the internal leaflet of the lipid membrane, may provide additional stabilization for the capsid. These results are consistent with the observations for other large, icosahedral dsDNA viruses that also utilize minor capsid proteins for stabilization and for determining their assembly.
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Affiliation(s)
- Xiaodong Yan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA
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43
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Plevka P, Tars K, Liljas L. Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles. Protein Sci 2008; 17:1731-9. [PMID: 18662904 PMCID: PMC2548359 DOI: 10.1110/ps.036905.108] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles.
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Affiliation(s)
- Pavel Plevka
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, LV 1067 Riga, Latvia
| | - Lars Liljas
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
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44
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The Anti-cancer Drug Chlorambucil as a Substrate for the Human Polymorphic Enzyme Glutathione Transferase P1-1: Kinetic Properties and Crystallographic Characterisation of Allelic Variants. J Mol Biol 2008; 380:131-44. [DOI: 10.1016/j.jmb.2008.04.066] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 04/14/2008] [Accepted: 04/16/2008] [Indexed: 10/22/2022]
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45
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Silvaggi NR, Wilson D, Tzipori S, Allen KN. Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex. Biochemistry 2008; 47:5736-45. [PMID: 18457419 DOI: 10.1021/bi8001067] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Clostridium botulinum neurotoxin serotype A light chain (BoNT/A-LC) is a Zn(II)-dependent metalloprotease that blocks the release of acetylcholine at the neuromuscular junction by cleaving SNAP-25, one of the SNARE proteins required for exocytosis. Because of the potential for use of the toxin in bioterrorism and the increasingly widespread application of the toxin in the medical field, there is significant interest in the development of small-molecule inhibitors of the metalloprotease. Efforts to design such inhibitors have not benefited from knowledge of how peptides bind to the active site since the enzyme-peptide structures available previously either were not occupied in the vicinity of the catalytic Zn(II) ion or did not represent the product of SNAP-25 substrate cleavage. Herein we report the 1.4 A-resolution X-ray crystal structure of a complex between the BoNT/A-LC and the inhibitory peptide N-Ac-CRATKML, the first structure of the light chain with an inhibitory peptide bound at the catalytic Zn(II) ion. The peptide is bound with the Cys S gamma atom coordinating the metal ion. Surprisingly, the cysteine sulfur is oxidized to the sulfenic acid form. Given the unstable nature of this species in solution, is it likely that oxidation occurs on the enzyme. In addition to the peptide-bound structure, we report two structures of the unliganded light chain with and without the Zn(II) cofactor bound at 1.25 and 1.20 A resolution, respectively. The two structures are nearly identical, confirming that the Zn(II) ion plays a purely catalytic role. Additionally, the structure of the Zn(II)-bound uncomplexed enzyme allows identification of the catalytic water molecule and a second water molecule that occupies the same position as the peptidic oxygen in the tetrahedral intermediate. This observation suggests that the enzyme active site is prearranged to stabilize the tetrahedral intermediate of the protease reaction.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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46
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Shin DH, Proudfoot M, Lim HJ, Choi IK, Yokota H, Yakunin AF, Kim R, Kim SH. Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans. Proteins 2008; 70:1000-9. [PMID: 17847097 DOI: 10.1002/prot.21584] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have determined the crystal structure of DR1281 from Deinococcus radiodurans. DR1281 is a protein of unknown function with over 170 homologs found in prokaryotes and eukaryotes. To elucidate the molecular function of DR1281, its crystal structure at 2.3 A resolution was determined and a series of biochemical screens for catalytic activity was performed. The crystal structure shows that DR1281 has two domains, a small alpha domain and a putative catalytic domain formed by a four-layered structure of two beta-sheets flanked by five alpha-helices on both sides. The small alpha domain interacts with other molecules in the asymmetric unit and contributes to the formation of oligomers. The structural comparison of the putative catalytic domain with known structures suggested its biochemical function to be a phosphatase, phosphodiesterase, nuclease, or nucleotidase. Structural analyses with its homologues also indicated that there is a dinuclear center at the interface of two domains formed by Asp8, Glu37, Asn38, Asn65, His148, His173, and His175. An absolute requirement of metal ions for activity has been proved by enzymatic assay with various divalent metal ions. A panel of general enzymatic assays of DR1281 revealed metal-dependent catalytic activity toward model substrates for phosphatases (p-nitrophenyl phosphate) and phosphodiesterases (bis-p-nitrophenyl phosphate). Subsequent secondary enzymatic screens with natural substrates demonstrated significant phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP. Thus, our structural and enzymatic studies have identified the biochemical function of DR1281 as a novel phosphatase/phosphodiesterase and disclosed key conserved residues involved in metal binding and catalytic activity.
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Affiliation(s)
- Dong Hae Shin
- College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea.
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47
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Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit. Proc Natl Acad Sci U S A 2008; 105:500-5. [PMID: 18187576 DOI: 10.1073/pnas.0711076105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, two crystal structures of the Thermus thermophilus 70S ribosome in the same functional state were determined at 2.8 and 3.7 A resolution but were different throughout. The most functionally significant structural differences are in the conformation of the peptidyl-transferase center (PTC) and the interface between the PTC and the CCA end of the P-site tRNA. Likewise, the 3.7 A PTC differed from the functionally equivalent structure of the Haloarcula marismortui 50S subunit. To ascertain whether the 3.7 A model does indeed differ from the other two, we performed cross-crystal averaging of the two 70S data sets. The unbiased maps suggest that the conformation of the PTC-CCA in the two 70S crystal forms is identical to that of the 2.8 A 70S model as well as that of the H. marismortui 50S subunit. We conclude that the structure of the PTC is the same in the functionally equivalent 70S ribosome and the 50S subunit.
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Xiong Y. From electron microscopy to X-ray crystallography: molecular-replacement case studies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:76-82. [PMID: 18094470 PMCID: PMC2394795 DOI: 10.1107/s090744490705398x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 10/29/2007] [Indexed: 11/16/2022]
Abstract
Multi-component molecular complexes are increasingly being tackled by structural biology, bringing X-ray crystallography into the purview of electron-microscopy (EM) studies. X-ray crystallography can utilize a low-resolution EM map for structure determination followed by phase extension to high resolution. Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement (MR) using various standard MR packages such as AMoRe, MOLREP and Phaser. The results demonstrate that EM maps are viable models for molecular replacement. Possible difficulties in data analysis, such as the effects of the EM magnification error, and the effect of MR positional/rotational errors on phase extension are discussed.
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Affiliation(s)
- Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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Anderson DH, Kickhoefer VA, Sievers SA, Rome LH, Eisenberg D. Draft crystal structure of the vault shell at 9-A resolution. PLoS Biol 2007; 5:e318. [PMID: 18044992 PMCID: PMC2229873 DOI: 10.1371/journal.pbio.0050318] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Accepted: 10/03/2007] [Indexed: 11/20/2022] Open
Abstract
Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-Å resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules. Vaults are large barrel-shaped particles found in the cytoplasm in all mammalian cells, which may function in innate immunity. As naturally occurring nanoscale capsules, vaults may be useful objects to engineer as delivery vehicles. In this study, we propose an atomic structure for the thin outer shell of the vault. Using x-ray diffraction and computer modeling, we have inferred a draft atomic model for the major vault protein, which forms the shell-like enclosure of the vault. The shell is made up of 96 identical protein chains, each of 873 amino acid residues, folded into 14 domains. Each chain forms an elongated stave of half the vault, as well as the cap of the barrel-like shell. Our draft atomic model is essentially an atomic-level model for the entire 9.3-MDa vault shell, which offers a guide for protein engineering to test vault functions and to exploit vault particles as nanocapsules. A draft atomic structure has been determined for the 9.3-MDa protein shell of the vault cytoplasmic particle, revealing stave-like polypeptides forming the barrel-like structure of the vault.
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Affiliation(s)
- Daniel H Anderson
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Valerie A Kickhoefer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stuart A Sievers
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Leonard H Rome
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - David Eisenberg
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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50
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Plevka P, Tars K, Zeltins A, Balke I, Truve E, Liljas L. The three-dimensional structure of ryegrass mottle virus at 2.9 A resolution. Virology 2007; 369:364-74. [PMID: 17881031 DOI: 10.1016/j.virol.2007.07.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 07/17/2007] [Indexed: 11/22/2022]
Abstract
The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has been determined at 2.9 A resolution. The coat protein has a canonical jellyroll beta-sandwich fold. In comparison to other sobemoviruses the RGMoV coat protein is missing several residues in two of the loop regions. The first loop contributes to contacts between subunits around the quasi-threefold symmetry axis. The altered contact interface results in tilting of the subunits towards the quasi-threefold axis. The assembly of the T=3 capsid of sobemoviruses is controlled by the N-termini of C subunits forming a so-called beta-annulus. The other loop that is smaller in the RGMoV structure contains a helix that participates in stabilization of the beta-annulus in other sobemoviruses. The loss of interaction between the RGMoV loop and the beta-annulus has been compensated for by additional interactions between the N-terminal arms. As a consequence of these differences, the diameter of the RGMoV particle is 8 A smaller than that of the other sobemoviruses. The interactions of coat proteins in sobemovirus capsids involve calcium ions. Depletion of calcium ions results in particle swelling, which is considered a first step in disassembly. We could not identify any density for metal ions in the proximity of the conserved residues normally involved in calcium binding, but the RGMoV structure does not show any signs of swelling. A likely reason is the low pH (3.0) of the crystallization buffer in which the groups interacting with the calcium ions are not charged.
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Affiliation(s)
- Pavel Plevka
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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