1301
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Lehneck R, Neumann P, Vullo D, Elleuche S, Supuran CT, Ficner R, Pöggeler S. Crystal structures of two tetrameric β-carbonic anhydrases from the filamentous ascomycete Sordaria macrospora. FEBS J 2014; 281:1759-72. [PMID: 24506675 DOI: 10.1111/febs.12738] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 01/11/2023]
Abstract
UNLABELLED Carbonic anhydrases (CAs) are metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate (hydrogen carbonate) and protons. CAs have been identified in archaea, bacteria and eukaryotes and can be classified into five groups (α, β, γ, δ, ζ) that are unrelated in sequence and structure. The fungal β-class has only recently attracted attention. In the present study, we investigated the structure and function of the plant-like β-CA proteins CAS1 and CAS2 from the filamentous ascomycete Sordaria macrospora. We demonstrated that both proteins can substitute for the Saccharomyces cerevisiae β-CA Nce103 and exhibit an in vitro CO2 hydration activity (kcat /Km of CAS1: 1.30 × 10(6) m(-1) ·s(-1) ; CAS2: 1.21 × 10(6 ) m(-1) ·s(-1) ). To further investigate the structural properties of CAS1 and CAS2, we determined their crystal structures to a resolution of 2.7 Å and 1.8 Å, respectively. The oligomeric state of both proteins is tetrameric. With the exception of the active site composition, no further major differences have been found. In both enzymes, the Zn(2) (+) -ion is tetrahedrally coordinated; in CAS1 by Cys45, His101 and Cys104 and a water molecule and in CAS2 by the side chains of four residues (Cys56, His112, Cys115 and Asp58). Both CAs are only weakly inhibited by anions, making them good candidates for industrial applications. STRUCTURED DIGITAL ABSTRACT CAS1 and CAS2 bind by x-ray crystallography (View interaction) DATABASE Structural data have been deposited in the Protein Data Bank database under accession numbers 4O1J for CAS1 and 4O1K for CAS2.
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Affiliation(s)
- Ronny Lehneck
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University Göttingen, Germany
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1302
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Maier S, Pflüger T, Loesgen S, Asmus K, Brötz E, Paululat T, Zeeck A, Andrade S, Bechthold A. Insights into the bioactivity of mensacarcin and epoxide formation by MsnO8. Chembiochem 2014; 15:749-56. [PMID: 24554499 DOI: 10.1002/cbic.201300704] [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: 11/08/2013] [Indexed: 12/12/2022]
Abstract
Mensacarcin, a potential antitumour drug, is produced by Streptomyces bottropensis. The structure consists of a three-membered ring system with many oxygen atoms. Of vital importance in this context is an epoxy moiety in the side chain of mensacarcin. Our studies with different mensacarcin derivatives have demonstrated that this epoxy group is primarily responsible for the cytotoxic effect of mensacarcin. In order to obtain further information about this epoxy moiety, inactivation experiments in the gene cluster were carried out to identify the epoxy-forming enzyme. Therefore the cosmid cos2, which covers almost the complete type II polyketide synthase (PKS) gene cluster, was heterologously expressed in Streptomyces albus. This led to production of didesmethylmensacarcin, due to the fact that methyltransferase genes are missing in the cosmid. Further gene inactivation experiments on this cosmid showed that MsnO8, a luciferase-like monooxygenase, introduces the epoxy group at the end of the biosynthesis of mensacarcin. In addition, the protein MsnO8 was purified, and its crystal structure was determined to a resolution of 1.80 Å.
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Affiliation(s)
- Sarah Maier
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
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1303
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Structure of the pseudokinase domain of BIR2, a regulator of BAK1-mediated immune signaling in Arabidopsis. J Struct Biol 2014; 186:112-21. [PMID: 24556575 DOI: 10.1016/j.jsb.2014.02.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 01/01/2023]
Abstract
The BAK1-interacting receptor-like kinase 2 (BIR2) belongs to the large family of leucine-rich repeat receptor-like kinases (LRR-RLKs) that mediate development and innate immunity in plants and form a monophyletic gene family with the Drosophila Pelle and human interleukin-1 receptor-associated kinases (IRAK). BIR2 is a negative regulator of BAK1-mediated defense mechanisms and cell death responses, yet key residues that are typically required for kinase activity are not present in the BIR2 kinase domain. We have determined the crystal structure of the BIR2 cytosolic domain and show that its nucleotide binding site is occluded. NMR spectroscopy confirmed that neither wild type nor phosphorylation-mimicking mutants of BIR2 bind ATP-analogues in solution, suggesting that BIR2 is a genuine enzymatically inactive pseudokinase. BIR2 is, however, phosphorylated by its target of regulation, BAK1. Using nano LC-MS/MS analysis for site-specific analysis of phosphorylation, we found a high density of BAK1-transphosphorylation sites in the BIR2 juxta membrane domain, a region previously implicated in regulation of RLKs. Our findings provide a structural basis to better understand signaling through kinase-dead domains that are predicted to account for 20% of all Arabidopsis RLKs and 10% of all human kinases.
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1304
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Domingo Meza-Aguilar J, Fromme P, Torres-Larios A, Mendoza-Hernández G, Hernandez-Chiñas U, Arreguin-Espinosa de Los Monteros RA, Eslava Campos CA, Fromme R. X-ray crystal structure of the passenger domain of plasmid encoded toxin(Pet), an autotransporter enterotoxin from enteroaggregative Escherichia coli (EAEC). Biochem Biophys Res Commun 2014; 445:439-44. [PMID: 24530907 DOI: 10.1016/j.bbrc.2014.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/05/2014] [Indexed: 01/29/2023]
Abstract
Autotransporters (ATs) represent a superfamily of proteins produced by a variety of pathogenic bacteria, which include the pathogenic groups of Escherichia coli (E. coli) associated with gastrointestinal and urinary tract infections. We present the first X-ray structure of the passenger domain from the Plasmid-encoded toxin (Pet) a 100 kDa protein at 2.3 Å resolution which is a cause of acute diarrhea in both developing and industrialized countries. Pet is a cytoskeleton-altering toxin that induces loss of actin stress fibers. While Pet (pdb code: 4OM9) shows only a sequence identity of 50% compared to the closest related protein sequence, extracellular serine protease plasmid (EspP) the structural features of both proteins are conserved. A closer structural look reveals that Pet contains a β-pleaded sheet at the sequence region of residues 181-190, the corresponding structural domain in EspP consists of a coiled loop. Secondary, the Pet passenger domain features a more pronounced beta sheet between residues 135 and 143 compared to the structure of EspP.
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Affiliation(s)
- J Domingo Meza-Aguilar
- Departamento de Salud Pública Facultad de Medicina UNAM, Ciudad Universitaria Coyoacán 04510, D.F., Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez 06720, D.F., Mexico
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Physical Sciences BLDG D-102, Tempe, AZ 85287, USA
| | - Alfredo Torres-Larios
- Instituto de Fisiología Celular UNAM, Ciudad Universitaria Coyoacán 04510, D.F., Mexico
| | | | - Ulises Hernandez-Chiñas
- Departamento de Salud Pública Facultad de Medicina UNAM, Ciudad Universitaria Coyoacán 04510, D.F., Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez 06720, D.F., Mexico
| | | | - Carlos A Eslava Campos
- Departamento de Salud Pública Facultad de Medicina UNAM, Ciudad Universitaria Coyoacán 04510, D.F., Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez 06720, D.F., Mexico
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Physical Sciences BLDG D-102, Tempe, AZ 85287, USA.
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1305
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Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole. J Biol Chem 2014; 289:8891-902. [PMID: 24519933 DOI: 10.1074/jbc.m113.509273] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sortase cysteine transpeptidases covalently attach proteins to the bacterial cell wall or assemble fiber-like pili that promote bacterial adhesion. Members of this enzyme superfamily are widely distributed in Gram-positive bacteria that frequently utilize multiple sortases to elaborate their peptidoglycan. Sortases catalyze transpeptidation using a conserved active site His-Cys-Arg triad that joins a sorting signal located at the C terminus of their protein substrate to an amino nucleophile located on the cell surface. However, despite extensive study, the catalytic mechanism and molecular basis of substrate recognition remains poorly understood. Here we report the crystal structure of the Staphylococcus aureus sortase B enzyme in a covalent complex with an analog of its NPQTN sorting signal substrate, revealing the structural basis through which it displays the IsdC protein involved in heme-iron scavenging from human hemoglobin. The results of computational modeling, molecular dynamics simulations, and targeted amino acid mutagenesis indicate that the backbone amide of Glu(224) and the side chain of Arg(233) form an oxyanion hole in sortase B that stabilizes high energy tetrahedral catalytic intermediates. Surprisingly, a highly conserved threonine residue within the bound sorting signal substrate facilitates construction of the oxyanion hole by stabilizing the position of the active site arginine residue via hydrogen bonding. Molecular dynamics simulations and primary sequence conservation suggest that the sorting signal-stabilized oxyanion hole is a universal feature of enzymes within the sortase superfamily.
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1306
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Luo Z, Rajashankar K, Dauter Z. Weak data do not make a free lunch, only a cheap meal. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:253-60. [PMID: 24531460 PMCID: PMC3940200 DOI: 10.1107/s1399004713026680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/27/2013] [Indexed: 11/10/2022]
Abstract
Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as Rmerge and I/σ(I), optical resolution and the correlation coefficients CC1/2 and CC*, can be used for judging the internal data quality, whereas the reliability factors R and Rfree as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where the I/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.
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Affiliation(s)
- Zhipu Luo
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 90439, USA
| | - Kanagalaghatta Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 90439, USA
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1307
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Abstract
INTRODUCTION X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule-ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. AREAS COVERED This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of 'Big Data' analysis, biochemical experimental design and structure-based drug discovery. EXPERT OPINION Although X-ray crystallography is one of the most detailed 'microscopes' available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify these hypotheses. X-ray crystallography will find its future application in drug discovery by the development of specific tools that would allow realistic interpretation of the outcome coordinates and/or support testing of these hypotheses.
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Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID)
- Midwest Center for Structural Genomics (MCSG), USA
- New York Structural Genomics Research Consortium (NYSGRC), USA
- Specializes in Protein Crystallography, Data Analytics and Data Mining, Research Scientist
| | - Jing Hou
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID)
- Enzyme Structure Initiative (EFI), USA
- New York Structural Genomics Research Consortium (NYSGRC), USA
- Specializes in Protein Crystallography, Research Associate
| | - Matthew D Zimmerman
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID)
- Enzyme Structure Initiative (EFI), USA
- Midwest Center for Structural Genomics (MCSG), USA
- New York Structural Genomics Research Consortium (NYSGRC), USA
- Specializes in Protein Crystallography, Data Mining and Management, Instructor of Research
| | - Alexander Wlodawer
- National Cancer Institute, Center for Cancer Research, Frederick, MD 21702, USA
- Specializes in Macromolecular Structure and Function, Chief of the Macromolecular Crystallography Laboratory
| | - Wladek Minor
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID)
- Enzyme Structure Initiative (EFI), USA
- Midwest Center for Structural Genomics (MCSG), USA
- New York Structural Genomics Research Consortium (NYSGRC), USA
- Specializes in Structural Biology, Data Mining and Management, Professor
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1308
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Kenny PW, Newman J, Peat TS. Nitrate in the active site of protein tyrosine phosphatase 1B is a putative mimetic of the transition state. ACTA ACUST UNITED AC 2014; 70:565-71. [PMID: 24531490 DOI: 10.1107/s1399004713031052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/12/2013] [Indexed: 11/10/2022]
Abstract
The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important WPD loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.
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Affiliation(s)
- Peter W Kenny
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
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1309
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Huang L, Lilley DMJ. Structure of a rare non-standard sequence k-turn bound by L7Ae protein. Nucleic Acids Res 2014; 42:4734-40. [PMID: 24482444 PMCID: PMC3985660 DOI: 10.1093/nar/gku087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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1310
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Functional implications of the binding mode of a human conformation-dependent V2 monoclonal antibody against HIV. J Virol 2014; 88:4100-12. [PMID: 24478429 DOI: 10.1128/jvi.03153-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
UNLABELLED Data from the RV144 HIV vaccine trial indicated that gp120 V2 antibodies were associated with a lower risk of infection; thus, the mapping of V2 epitopes can contribute to the design of an effective HIV vaccine. We solved the crystal structure of human monoclonal antibody (MAb) 2158, which targets a conformational V2 epitope overlapping the α4β7 integrin binding site, and constructed a full-length model of V1V2. Comparison of computational energy stability to experimental enzyme-linked immunosorbent assay (ELISA) results identified a hydrophobic core that stabilizes the V2 region for optimal 2158 binding, as well as residues that directly mediate side chain interactions with MAb 2158. These data define the binding surface recognized by MAb 2158 and offer a structural explanation for why a mismatched mutation at position 181 (I181X) in the V2 loop was associated with a higher vaccine efficiency in the RV144 clinical vaccine trial. IMPORTANCE Correlate analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the second variable region (V2) of HIV-1 gp120 was responsible for the modest protection observed in the trial. V2 is a highly variable and immunogenic region, and structural information on its antigenic landscape will be important for rational design of an effective HIV-1 vaccine. Using X-ray crystallography, computational design tools, and mutagenesis assays, we carried out a detailed and systematic investigation of the epitope recognition of human V2 MAb 2158 and demonstrated that its epitope region overlaps the integrin binding site within V2. In addition, we propose a structure-based mechanism for mismatching of the isoleucine at position 181 and the increased vaccine efficacy seen in the RV144 vaccine trial.
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1311
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Crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii. Antimicrob Agents Chemother 2014; 58:2135-43. [PMID: 24468777 DOI: 10.1128/aac.01983-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class D β-lactamases capable of hydrolyzing last-resort carbapenem antibiotics represent a major challenge for treatment of bacterial infections. Wide dissemination of these enzymes in Acinetobacter baumannii elevated this pathogen to the category of most deadly and difficult to treat. We present here the structure of the OXA-58 β-lactamase, a major class D carbapenemase of A. baumannii, determined to 1.30-Å resolution. Unlike two other Acinetobacter carbapenemases, OXA23 and OXA-24, the OXA-58 enzyme lacks the characteristic hydrophobic bridge over the active site, despite conservation of the residues which participate in its formation. The active-site residues in OXA-58 are spatially conserved in comparison to those in other class D β-lactamases. Lys86, which activates water molecules during the acylation and deacylation steps, is fully carboxylated in the OXA-58 structure. In the absence of a substrate, a water molecule is observed in the active site of the enzyme and is positioned in the pocket that is usually occupied by the 6α-hydroxyethyl moiety of carbapenems. A water molecule in this location would efficiently deacylate good substrates, such as the penicillins, but in the case of carbapenems, it would be expelled by the 6α-hydroxyethyl moiety of the antibiotics and a water from the surrounding medium would find its way to the vicinity of the carboxylated Lys86 to perform deacylation. Subtle differences in the position of this water in the acyl-enzyme complexes of class D β-lactamases could ultimately be responsible for differences in the catalytic efficiencies of these enzymes against last-resort carbapenem antibiotics.
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1312
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Juneja P, Rao A, Cölfen H, Diederichs K, Welte W. Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 from Strongylocentrotus purpuratus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:260-2. [PMID: 24637770 DOI: 10.1107/s2053230x14000880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022]
Abstract
Sea urchin spicules have a calcitic mesocrystalline architecture that is closely associated with a matrix of proteins and amorphous minerals. The mechanism underlying spicule formation involves complex processes encompassing spatio-temporally regulated organic-inorganic interactions. C-type lectin domains are present in several spicule matrix proteins in Strongylocentrotus purpuratus, implying their role in spiculogenesis. In this study, the C-type lectin domain of SM50 was overexpressed, purified and crystallized using a vapour-diffusion method. The crystal diffracted to a resolution of 2.85 Å and belonged to space group P212121, with unit-cell parameters a = 100.6, b = 115.4, c = 130.6 Å, α = β = γ = 90°. Assuming 50% solvent content, six chains are expected to be present in the asymmetric unit.
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Affiliation(s)
- Puneet Juneja
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Ashit Rao
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Wolfram Welte
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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1313
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Tan TC, Spadiut O, Gandini R, Haltrich D, Divne C. Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion. PLoS One 2014; 9:e86736. [PMID: 24466218 PMCID: PMC3897772 DOI: 10.1371/journal.pone.0086736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
Each year, about six million tons of lactose are generated from liquid whey as industrial byproduct, and optimally this large carbohydrate waste should be used for the production of value-added products. Trametes multicolor pyranose 2-oxidase (TmP2O) catalyzes the oxidation of various monosaccharides to the corresponding 2-keto sugars. Thus, a potential use of TmP2O is to convert the products from lactose hydrolysis, D-glucose and D-galactose, to more valuable products such as tagatose. Oxidation of glucose is however strongly favored over galactose, and oxidation of both substrates at more equal rates is desirable. Characterization of TmP2O variants (H450G, V546C, H450G/V546C) with improved D-galactose conversion has been given earlier, of which H450G displayed the best relative conversion between the substrates. To rationalize the changes in conversion rates, we have analyzed high-resolution crystal structures of the aforementioned mutants with bound 2- and 3-fluorinated glucose and galactose. Binding of glucose and galactose in the productive 2-oxidation binding mode is nearly identical in all mutants, suggesting that this binding mode is essentially unaffected by the mutations. For the competing glucose binding mode, enzyme variants carrying the H450G replacement stabilize glucose as the α-anomer in position for 3-oxidation. The backbone relaxation at position 450 allows the substrate-binding loop to fold tightly around the ligand. V546C however stabilize glucose as the β-anomer using an open loop conformation. Improved binding of galactose is enabled by subtle relaxation effects at key active-site backbone positions. The competing binding mode for galactose 2-oxidation by V546C stabilizes the β-anomer for oxidation at C1, whereas H450G variants stabilize the 3-oxidation binding mode of the galactose α-anomer. The present study provides a detailed description of binding modes that rationalize changes in the relative conversion rates of D-glucose and D-galactose and can be used to refine future enzyme designs for more efficient use of lactose-hydrolysis byproducts.
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Affiliation(s)
- Tien Chye Tan
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Oliver Spadiut
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Rosaria Gandini
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Divne
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden ; School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
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1314
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Chadegani F, Lovell S, Mullangi V, Miyagi M, Battaile KP, Bann JG. (19)F nuclear magnetic resonance and crystallographic studies of 5-fluorotryptophan-labeled anthrax protective antigen and effects of the receptor on stability. Biochemistry 2014; 53:690-701. [PMID: 24387629 PMCID: PMC3985773 DOI: 10.1021/bi401405s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The anthrax protective antigen (PA)
is an 83 kDa protein that is
one of three protein components of the anthrax toxin, an AB toxin
secreted by Bacillus anthracis. PA is capable of
undergoing several structural changes, including oligomerization to
either a heptameric or octameric structure called the prepore, and
at acidic pH a major conformational change to form a membrane-spanning
pore. To follow these structural changes at a residue-specific level,
we have conducted initial studies in which we have biosynthetically
incorporated 5-fluorotryptophan (5-FTrp) into PA, and we have studied
the influence of 5-FTrp labeling on the structural stability of PA
and on binding to the host receptor capillary morphogenesis protein
2 (CMG2) using 19F nuclear magnetic resonance (NMR). There
are seven tryptophans in PA, but of the four domains in PA, only two
contain tryptophans: domain 1 (Trp65, -90, -136, -206, and -226) and
domain 2 (Trp346 and -477). Trp346 is of particular interest because
of its proximity to the CMG2 binding interface, and because it forms
part of the membrane-spanning pore. We show that the 19F resonance of Trp346 is sensitive to changes in pH, consistent with
crystallographic studies, and that receptor binding significantly
stabilizes Trp346 to both pH and temperature. In addition, we provide
evidence that suggests that resonances from tryptophans distant from
the binding interface are also stabilized by the receptor. Our studies
highlight the positive impact of receptor binding on protein stability
and the use of 19F NMR in gaining insight into structural
changes in a high-molecular weight protein.
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Affiliation(s)
- Fatemeh Chadegani
- Department of Chemistry, Wichita State University , Wichita, Kansas 67260, United States
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1315
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Barta ML, Lovell S, Sinclair AN, Battaile KP, Hefty PS. Chlamydia trachomatis CT771 (nudH) is an asymmetric Ap4A hydrolase. Biochemistry 2014; 53:214-24. [PMID: 24354275 DOI: 10.1021/bi401473e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Asymmetric diadenosine 5',5‴-P(1),P(4)-tetraphosphate (Ap4A) hydrolases are members of the Nudix superfamily that asymmetrically cleave the metabolite Ap4A into ATP and AMP while facilitating homeostasis. The obligate intracellular mammalian pathogen Chlamydia trachomatis possesses a single Nudix family protein, CT771. As pathogens that rely on a host for replication and dissemination typically have one or zero Nudix family proteins, this suggests that CT771 could be critical for chlamydial biology and pathogenesis. We identified orthologues to CT771 within environmental Chlamydiales that share active site residues suggesting a common function. Crystal structures of both apo- and ligand-bound CT771 were determined to 2.6 Å and 1.9 Å resolution, respectively. The structure of CT771 shows a αβα-sandwich motif with many conserved elements lining the putative Nudix active site. Numerous aspects of the ligand-bound CT771 structure mirror those observed in the ligand-bound structure of the Ap4A hydrolase from Caenorhabditis elegans. These structures represent only the second Ap4A hydrolase enzyme member determined from eubacteria and suggest that mammalian and bacterial Ap4A hydrolases might be more similar than previously thought. The aforementioned structural similarities, in tandem with molecular docking, guided the enzymatic characterization of CT771. Together, these studies provide the molecular details for substrate binding and specificity, supporting the analysis that CT771 is an Ap4A hydrolase (nudH).
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Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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1316
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Khoshnevis S, Gunišová S, Vlčková V, Kouba T, Neumann P, Beznosková P, Ficner R, Valášek LS. Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes. Nucleic Acids Res 2014; 42:4123-39. [PMID: 24423867 PMCID: PMC3973348 DOI: 10.1093/nar/gkt1369] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 43–48S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65-Å resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs.
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Affiliation(s)
- Sohail Khoshnevis
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, George-August University, Goettingen, Germany, 37077 and Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, the Czech Republic
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1317
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Highly reinforced structure of a C-terminal dimerization domain in von Willebrand factor. Blood 2014; 123:1785-93. [PMID: 24394662 DOI: 10.1182/blood-2013-11-523639] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-terminal cystine knot (CK) (CTCK) domain in von Willebrand factor (VWF) mediates dimerization of proVWF in the endoplasmic reticulum and is essential for long multimers required for hemostatic function. The CTCK dimer crystal structure reveals highly elongated monomers with 2 β-ribbons and 4 intra-chain disulfides, including 3 in the CK. Dimerization buries an extensive interface of 1500 Å(2) corresponding to 32% of the surface of each monomer and forms a super β-sheet and 3 inter-chain disulfides. The shape, dimensions, and N-terminal connections of the crystal structure agree perfectly with previous electron microscopic images of VWF dimeric bouquets with the CTCK dimer forming a down-curved base. The dimer interface is suited to resist hydrodynamic force and disulfide reduction. CKs in each monomer flank the 3 inter-chain disulfides, and their presence in β-structures with dense backbone hydrogen bonds creates a rigid, highly crosslinked interface. The structure reveals the basis for von Willebrand disease phenotypes and the fold and disulfide linkages for CTCK domains in diverse protein families involved in barrier function, eye and inner ear development, insect coagulation and innate immunity, axon guidance, and signaling in extracellular matrices.
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1318
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Blenner MA, Dong X, Springer TA. Structural basis of regulation of von Willebrand factor binding to glycoprotein Ib. J Biol Chem 2014; 289:5565-79. [PMID: 24391089 DOI: 10.1074/jbc.m113.511220] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation by elongational flow of von Willebrand factor (VWF) is critical for primary hemostasis. Mutations causing type 2B von Willebrand disease (VWD), platelet-type VWD (PT-VWD), and tensile force each increase affinity of the VWF A1 domain and platelet glycoprotein Ibα (GPIbα) for one another; however, the structural basis for these observations remains elusive. Directed evolution was used to discover a further gain-of-function mutation in A1 that shifts the long range disulfide bond by one residue. We solved multiple crystal structures of this mutant A1 and A1 containing two VWD mutations complexed with GPIbα containing two PT-VWD mutations. We observed a gained interaction between A1 and the central leucine-rich repeats (LRRs) of GPIbα, previously shown to be important at high shear stress, and verified its importance mutationally. These findings suggest that structural changes, including central GPIbα LRR-A1 contact, contribute to VWF affinity regulation. Among the mutant complexes, variation in contacts and poor complementarity between the GPIbα β-finger and the region of A1 harboring VWD mutations lead us to hypothesize that the structures are on a pathway to, but have not yet reached, a force-induced super high affinity state.
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Affiliation(s)
- Mark A Blenner
- From the Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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1319
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Hofbauer S, Gysel K, Bellei M, Hagmüller A, Schaffner I, Mlynek G, Kostan J, Pirker KF, Daims H, Furtmüller PG, Battistuzzi G, Djinović-Carugo K, Obinger C. Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity. Biochemistry 2014; 53:77-89. [PMID: 24364531 PMCID: PMC3893830 DOI: 10.1021/bi401042z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Chlorite dismutases (Clds) are heme b containing
oxidoreductases that convert chlorite to chloride and molecular oxygen.
In order to elucidate the role of conserved heme cavity residues in
the catalysis of this reaction comprehensive mutational and biochemical
analyses of Cld from “Candidatus Nitrospira
defluvii” (NdCld) were performed. Particularly, point mutations
of the cavity-forming residues R173, K141, W145, W146, and E210 were
performed. The effect of manipulation in 12 single and double mutants
was probed by UV–vis spectroscopy, spectroelectrochemistry,
pre-steady-state and steady-state kinetics, and X-ray crystallography.
Resulting biochemical data are discussed with respect to the known
crystal structure of wild-type NdCld and the variants R173A and R173K
as well as the structures of R173E, W145V, W145F, and the R173Q/W146Y
solved in this work. The findings allow a critical analysis of the
role of these heme cavity residues in the reaction mechanism of chlorite
degradation that is proposed to involve hypohalous acid as transient
intermediate and formation of an O=O bond. The distal R173
is shown to be important (but not fully essential) for the reaction
with chlorite, and, upon addition of cyanide, it acts as a proton
acceptor in the formation of the resulting low-spin complex. The proximal
H-bonding network including K141-E210-H160 keeps the enzyme in its
ferric (E°′ = −113 mV) and mainly
five-coordinated high-spin state and is very susceptible to perturbation.
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Affiliation(s)
- Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences , A-1190 Vienna, Austria
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1320
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Nguyen THD, Li J, Galej WP, Oshikane H, Newman AJ, Nagai K. Structural basis of Brr2-Prp8 interactions and implications for U5 snRNP biogenesis and the spliceosome active site. Structure 2014; 21:910-19. [PMID: 23727230 PMCID: PMC3677097 DOI: 10.1016/j.str.2013.04.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/08/2013] [Accepted: 04/19/2013] [Indexed: 12/12/2022]
Abstract
The U5 small nuclear ribonucleoprotein particle (snRNP) helicase Brr2 disrupts the U4/U6 small nuclear RNA (snRNA) duplex and allows U6 snRNA to engage in an intricate RNA network at the active center of the spliceosome. Here, we present the structure of yeast Brr2 in complex with the Jab1/MPN domain of Prp8, which stimulates Brr2 activity. Contrary to previous reports, our crystal structure and mutagenesis data show that the Jab1/MPN domain binds exclusively to the N-terminal helicase cassette. The residues in the Jab1/MPN domain, whose mutations in human Prp8 cause the degenerative eye disease retinitis pigmentosa, are found at or near the interface with Brr2, clarifying its molecular pathology. In the cytoplasm, Prp8 forms a precursor complex with U5 snRNA, seven Sm proteins, Snu114, and Aar2, but after nuclear import, Brr2 replaces Aar2 to form mature U5 snRNP. Our structure explains why Aar2 and Brr2 are mutually exclusive and provides important insights into the assembly of U5 snRNP. We report the structure of Brr2 helicase in complex with the Jab1/MPN domain of Prp8 Retinitis pigmentosa mutations in the Jab1/MPN domain of Prp8 disrupt this complex Mechanism is proposed for the U4/U6 snRNA duplex unwinding and spliceosome activation The Brr2-Jab1/MPN and Aar2-Prp8 complexes provide insight into U5 snRNP biogenesis
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1321
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Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase. Structure 2014; 22:315-25. [PMID: 24389024 DOI: 10.1016/j.str.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/23/2013] [Accepted: 12/06/2013] [Indexed: 11/21/2022]
Abstract
The 3'-terminal CCA (CCA-3' at positions 74-76) of tRNA is synthesized by CCA-adding enzyme using CTP and ATP as substrates, without a nucleic acid template. In Aquifex aeolicus, CC-adding and A-adding enzymes collaboratively synthesize the CCA-3'. The mechanism of CCA-3' synthesis by these two enzymes remained obscure. We now present crystal structures representing CC addition onto tRNA by A. aeolicus CC-adding enzyme. After C₇₄ addition in an enclosed active pocket and pyrophosphate release, the tRNA translocates and rotates relative to the enzyme, and C₇₅ addition occurs in the same active pocket as C₇₄ addition. At both the C₇₄-adding and C₇₅-adding stages, CTP is selected by Watson-Crick-like hydrogen bonds between the cytosine of CTP and conserved Asp and Arg residues in the pocket. After C₇₄C₇₅ addition and pyrophosphate release, the tRNA translocates further and drops off the enzyme, and the CC-adding enzyme terminates RNA polymerization.
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1322
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Domagalski MJ, Zheng H, Zimmerman MD, Dauter Z, Wlodawer A, Minor W. The quality and validation of structures from structural genomics. Methods Mol Biol 2014; 1091:297-314. [PMID: 24203341 DOI: 10.1007/978-1-62703-691-7_21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein-ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement.
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Affiliation(s)
- Marcin J Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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1323
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Prokofev II, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil. Acta Crystallogr F Struct Biol Commun 2014; 70:60-3. [PMID: 24419619 PMCID: PMC3943090 DOI: 10.1107/s2053230x13031877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022] Open
Abstract
Uridine phosphorylase catalyzes the phosphorolysis of ribonucleosides, with the nitrogenous base and ribose 1-phosphate as products. Additionally, it catalyzes the reverse reaction of the synthesis of ribonucleosides from ribose 1-phosphate and a nitrogenous base. However, the enzyme does not catalyze the synthesis of nucleosides when the substrate is a nitrogenous base substituted at the 6-position, such as 6-methyluracil (6-MU). In order to explain this fact, it is essential to investigate the three-dimensional structure of the complex of 6-MU with uridine phosphorylase. 6-MU is a pharmaceutical agent that improves tissue nutrition and enhances cell regeneration by normalization of nucleotide exchange in humans. 6-MU is used for the treatment of diseases of the gastrointestinal tract, including infectious diseases. Here, procedures to obtain the uridine phosphorylase from the pathogenic bacterium Vibrio cholerae (VchUPh), purification of this enzyme, crystallization of the complex of VchUPh with 6-MU, and X-ray data collection and preliminary X-ray analysis of the VchUPh-6-MU complex at atomic resolution are reported.
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Affiliation(s)
- Igor I. Prokofev
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Mariya V. Dontsova
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Tatyana A. Seregina
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Alexander S. Mironov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | | | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
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1324
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Nisemblat S, Parnas A, Yaniv O, Azem A, Frolow F. Crystallization and structure determination of a symmetrical 'football' complex of the mammalian mitochondrial Hsp60-Hsp10 chaperonins. Acta Crystallogr F Struct Biol Commun 2014; 70:116-9. [PMID: 24419632 PMCID: PMC3943094 DOI: 10.1107/s2053230x1303389x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/15/2013] [Indexed: 11/10/2022] Open
Abstract
The mitochondrial Hsp60-Hsp10 complex assists the folding of various proteins impelled by ATP hydrolysis, similar to the bacterial chaperonins GroEL and GroES. The near-atomic structural details of the mitochondrial chaperonins are not known, despite the fact that almost two decades have passed since the structures of the bacterial chaperonins became available. Here, the crystallization procedure, diffraction experiments and structure determination by molecular replacement of the mammalian mitochondrial chaperonin HSP60 (E321K mutant) and its co-chaperonin Hsp10 are reported.
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Affiliation(s)
- Shahar Nisemblat
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
- The Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Avital Parnas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
- The Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Oren Yaniv
- The Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Abdussalam Azem
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
- The Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Felix Frolow
- The Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
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1325
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Methods to refine macromolecular structures in cases of severe diffraction anisotropy. Methods Mol Biol 2014; 1091:205-14. [PMID: 24203335 DOI: 10.1007/978-1-62703-691-7_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Diffraction anisotropy is characterized by variation in diffraction quality with reciprocal lattice direction. In the example presented here, diffraction extended to 2.1 Å resolution along a* and c* directions but only to 3.0 Å along the b* direction. Severe anisotropy such as this is often associated with lack of detail in electron density maps, stalled model improvement, and poor refinement statistics. Published methods for overcoming these difficulties have been combined and implemented in the diffraction anisotropy server. Specifically, the server offers information to diagnose the degree of anisotropy, and then applies ellipsoidal resolution boundaries, anisotropic scaling, and B-factor sharpening to the data set to compensate for the deleterious effects of diffraction anisotropy. Here, I offer advice on implementing these methods to facilitate refinement of macromolecular structures in cases of severely anisotropic data.
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1326
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Ruskamo S, Yadav RP, Sharma S, Lehtimäki M, Laulumaa S, Aggarwal S, Simons M, Bürck J, Ulrich AS, Juffer AH, Kursula I, Kursula P. Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:165-76. [PMID: 24419389 PMCID: PMC3919267 DOI: 10.1107/s1399004713027910] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/11/2013] [Indexed: 01/03/2023]
Abstract
P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structural analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.
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Affiliation(s)
- Salla Ruskamo
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ravi P. Yadav
- Molecular Biology Unit, Institute of Medical Sciences (IMS), Banaras Hindu University, Varanasi, India
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Satyan Sharma
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mari Lehtimäki
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Saara Laulumaa
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Shweta Aggarwal
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Mikael Simons
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute for Technology (KIT), Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute for Technology (KIT), Karlsruhe, Germany
| | - André H. Juffer
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Inari Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
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1327
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Niemann V, Koch-Singenstreu M, Neu A, Nilkens S, Götz F, Unden G, Stehle T. The NreA protein functions as a nitrate receptor in the staphylococcal nitrate regulation system. J Mol Biol 2013; 426:1539-53. [PMID: 24389349 DOI: 10.1016/j.jmb.2013.12.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 02/04/2023]
Abstract
Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35Å resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22μM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.
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Affiliation(s)
- Volker Niemann
- Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany
| | - Mareike Koch-Singenstreu
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - Ancilla Neu
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Stephanie Nilkens
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany
| | - Friedrich Götz
- Interfaculty Institute of Microbiology and Infection Medicine, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Gottfried Unden
- Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany.
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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1328
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Grishin AM, Cherney M, Anderson DH, Phanse S, Babu M, Cygler M. NleH defines a new family of bacterial effector kinases. Structure 2013; 22:250-9. [PMID: 24373767 DOI: 10.1016/j.str.2013.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 11/16/2022]
Abstract
Upon host cell infection, pathogenic Escherichia coli hijacks host cellular processes with the help of 20-60 secreted effector proteins that subvert cellular processes to create an environment conducive to bacterial survival. The NleH effector kinases manipulate the NF-κB pathway and prevent apoptosis. They show low sequence similarity to human regulatory kinases and contain two domains, the N-terminal, likely intrinsically unfolded, and a C-terminal kinase-like domain. We show that these effectors autophosphorylate on sites located predominantly in the N-terminal segment. The kinase domain displays a minimal kinase fold, but lacks an activation loop and the GHI subdomain. Nevertheless, all catalytically important residues are conserved. ATP binding proceeds with minimal structural rearrangements. The NleH structure is the first for the bacterial effector kinases family. NleHs and their homologous effector kinases form a new kinase family within the cluster of eukaryotic-like kinases that includes also Rio, Bud32, and KdoK families.
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Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
| | - Maia Cherney
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Deborah H Anderson
- Cancer Research, Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Research and Innovation Centre, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; Department of Biochemistry, McGill University, 3655 Promenade Sir Willam Osler, Montreal, QC H3G 1Y6, Canada.
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1329
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Niegowski D, Kleinschmidt T, Olsson U, Ahmad S, Rinaldo-Matthis A, Haeggström JZ. Crystal structures of leukotriene C4 synthase in complex with product analogs: implications for the enzyme mechanism. J Biol Chem 2013; 289:5199-207. [PMID: 24366866 PMCID: PMC3931076 DOI: 10.1074/jbc.m113.534628] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Leukotriene (LT) C4 synthase (LTC4S) catalyzes the conjugation of the fatty acid LTA4 with the tripeptide GSH to produce LTC4, the parent compound of the cysteinyl leukotrienes, important mediators of asthma. Here we mutated Trp-116 in human LTC4S, a residue proposed to play a key role in substrate binding, into an Ala or Phe. Biochemical and structural characterization of these mutants along with crystal structures of the wild type and mutated enzymes in complex with three product analogs, viz. S-hexyl-, 4-phenyl-butyl-, and 2-hydroxy-4-phenyl-butyl-glutathione, provide new insights to binding of substrates and product, identify a new conformation of the GSH moiety at the active site, and suggest a route for product release, aided by Trp-116.
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Affiliation(s)
- Damian Niegowski
- From the Division of Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-107 77 Stockholm, Sweden
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1330
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Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G, Weierstall U, Katritch V, Barty A, Zatsepin NA, Li D, Messerschmidt M, Boutet S, Williams GJ, Koglin JE, Seibert MM, Wang C, Shah ST, Basu S, Fromme R, Kupitz C, Rendek KN, Grotjohann I, Fromme P, Kirian RA, Beyerlein KR, White TA, Chapman HN, Caffrey M, Spence JC, Stevens RC, Cherezov V. Serial femtosecond crystallography of G protein-coupled receptors. Science 2013; 342:1521-4. [PMID: 24357322 PMCID: PMC3902108 DOI: 10.1126/science.1244142] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.
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Affiliation(s)
- Wei Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Wacker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Gye Won Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Vsevolod Katritch
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Dianfan Li
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Chong Wang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Syed T.A. Shah
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Kimberley N. Rendek
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Ingo Grotjohann
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Richard A. Kirian
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | | | - Thomas A. White
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free Electron Laser Science, DESY, 22607 Hamburg, Germany
- Institute for Experimental Physics, University of Hamburg, 22761 Hamburg, Germany
- Center for Ultrafast Imaging, 22607 Hamburg, Germany
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland
| | - John C.H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Raymond C. Stevens
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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1331
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Zahm JA, Padrick SB, Chen Z, Pak CW, Yunus AA, Henry L, Tomchick DR, Chen Z, Rosen MK. The bacterial effector VopL organizes actin into filament-like structures. Cell 2013; 155:423-34. [PMID: 24120140 DOI: 10.1016/j.cell.2013.09.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/22/2013] [Accepted: 09/11/2013] [Indexed: 12/28/2022]
Abstract
VopL is an effector protein from Vibrio parahaemolyticus that nucleates actin filaments. VopL consists of a VopL C-terminal domain (VCD) and an array of three WASP homology 2 (WH2) motifs. Here, we report the crystal structure of the VCD dimer bound to actin. The VCD organizes three actin monomers in a spatial arrangement close to that found in the canonical actin filament. In this arrangement, WH2 motifs can be modeled into the binding site of each actin without steric clashes. The data suggest a mechanism of nucleation wherein VopL creates filament-like structures, organized by the VCD with monomers delivered by the WH2 array, that can template addition of new subunits. Similarities with Arp2/3 complex and formin proteins suggest that organization of monomers into filament-like structures is a general and central feature of actin nucleation.
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Affiliation(s)
- Jacob A Zahm
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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1332
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Peng WC, de Lau W, Madoori PK, Forneris F, Granneman JCM, Clevers H, Gros P. Structures of Wnt-antagonist ZNRF3 and its complex with R-spondin 1 and implications for signaling. PLoS One 2013; 8:e83110. [PMID: 24349440 PMCID: PMC3861454 DOI: 10.1371/journal.pone.0083110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 10/30/2013] [Indexed: 01/10/2023] Open
Abstract
Zinc RING finger 3 (ZNRF3) and its homolog RING finger 43 (RNF43) antagonize Wnt signaling in adult stem cells by ubiquitinating Frizzled receptors (FZD), which leads to endocytosis of the Wnt receptor. Conversely, binding of ZNRF3/RNF43 to LGR4-6 – R-spondin blocks Frizzled ubiquitination and enhances Wnt signaling. Here, we present crystal structures of the ZNRF3 ectodomain and its complex with R-spondin 1 (RSPO1). ZNRF3 binds RSPO1 and LGR5-RSPO1 with micromolar affinity via RSPO1 furin-like 1 (Fu1) domain. Anonychia-related mutations in RSPO4 support the importance of the observed interface. The ZNRF3-RSPO1 structure resembles that of LGR5-RSPO1-RNF43, though Fu2 of RSPO1 is variably oriented. The ZNRF3-binding site overlaps with trans-interactions observed in 2:2 LGR5-RSPO1 complexes, thus binding of ZNRF3/RNF43 would disrupt such an arrangement. Sequence conservation suggests a single ligand-binding site on ZNRF3, consistent with the proposed competing binding role of ZNRF3/RNF43 in Wnt signaling.
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Affiliation(s)
- Weng Chuan Peng
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Wim de Lau
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Pramod K Madoori
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Federico Forneris
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Joke C M Granneman
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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1333
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Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A. Structural insights into DNA replication without hydrogen bonds. J Am Chem Soc 2013; 135:18637-43. [PMID: 24283923 PMCID: PMC3982147 DOI: 10.1021/ja409609j] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.
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Affiliation(s)
- Karin Betz
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Denis A. Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Thomas Lavergne
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Wolfram Welte
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Kay Diederichs
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Andreas Marx
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
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1334
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Wu Y, West AP, Kim HJ, Thornton ME, Ward AB, Bjorkman PJ. Structural basis for enhanced HIV-1 neutralization by a dimeric immunoglobulin G form of the glycan-recognizing antibody 2G12. Cell Rep 2013; 5:1443-55. [PMID: 24316082 DOI: 10.1016/j.celrep.2013.11.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/25/2013] [Accepted: 11/06/2013] [Indexed: 11/29/2022] Open
Abstract
The human immunoglobulin G (IgG) 2G12 recognizes high-mannose carbohydrates on the HIV type 1 (HIV-1) envelope glycoprotein gp120. Its two antigen-binding fragments (Fabs) are intramolecularly domain exchanged, resulting in a rigid (Fab)2 unit including a third antigen-binding interface not found in antibodies with flexible Fab arms. We determined crystal structures of dimeric 2G12 IgG created by intermolecular domain exchange, which exhibits increased breadth and >50-fold increased neutralization potency compared with monomeric 2G12. The four Fab and two fragment crystalline (Fc) regions of dimeric 2G12 were localized at low resolution in two independent structures, revealing IgG dimers with two (Fab)2 arms analogous to the Fabs of conventional monomeric IgGs. Structures revealed three conformationally distinct dimers, demonstrating flexibility of the (Fab)2-Fc connections that was confirmed by electron microscopy, small-angle X-ray scattering, and binding studies. We conclude that intermolecular domain exchange, flexibility, and bivalent binding to allow avidity effects are responsible for the increased potency and breadth of dimeric 2G12.
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Affiliation(s)
- Yunji Wu
- Division of Biology and Biological Engineering 114-96, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Anthony P West
- Division of Biology and Biological Engineering 114-96, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Helen J Kim
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew E Thornton
- Division of Biology and Biological Engineering 114-96, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering 114-96, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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1335
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Thomsen M, Skalden L, Palm GJ, Höhne M, Bornscheuer UT, Hinrichs W. Crystallization and preliminary X-ray diffraction studies of the (R)-selective amine transaminase from Aspergillus fumigatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1415-7. [PMID: 24316843 PMCID: PMC3855733 DOI: 10.1107/s1744309113030923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/11/2013] [Indexed: 11/11/2022]
Abstract
The (R)-selective amine transaminase from Aspergillus fumigatus was expressed in Escherichia coli and purified to homogeneity. Bright yellow crystals appeared while storing the concentrated solution in the refrigerator and belonged to space group C222(1). X-ray diffraction data were collected to 1.27 Å resolution, as well as an anomalous data set to 1.84 Å resolution that was suitable for S-SAD phasing.
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Affiliation(s)
- Maren Thomsen
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Lilly Skalden
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Gottfried J. Palm
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Matthias Höhne
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
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1336
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Tsurumura T, Qiu H, Yoshida T, Tsumori Y, Hatakeyama D, Kuzuhara T, Tsuge H. Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. PLoS One 2013; 8:e82020. [PMID: 24312396 PMCID: PMC3843726 DOI: 10.1371/journal.pone.0082020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/28/2013] [Indexed: 01/07/2023] Open
Abstract
Influenza pandemics with human-to-human transmission of the virus are of great public concern. It is now recognized that a number of factors are necessary for human transmission and virulence, including several key mutations within the PB2 subunit of RNA-dependent RNA polymerase. The structure of the middle domain in PB2 has been revealed with or without m(7)GTP, thus the middle domain is considered to be novel target for structure-based drug design. Here we report the crystal structure of the middle domain of H1N1 PB2 with or without m(7)GTP at 1.9 Å and 2.0 Å resolution, respectively, which has two mutations (P453H, I471T) to increase electrostatic potential and solubility. Here we report the m(7)GTP has unique conformation differ from the reported structure. 7-methyl-guanine is fixed in the pocket, but particularly significant change is seen in ribose and triphosphate region: the buried 7-methyl-guanine indeed binds in the pocket forming by H357, F404, E361 and K376 but the triphosphate continues directly to the outer domain. The presented conformation of m(7)GTP may be a clue for the anti-influenza drug-design.
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Affiliation(s)
- Toshiharu Tsurumura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Hao Qiu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Toru Yoshida
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Yayoi Tsumori
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Dai Hatakeyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
| | - Takashi Kuzuhara
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
- * E-mail:
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1337
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Batabyal D, Poulos TL. Crystal structures and functional characterization of wild-type CYP101D1 and its active site mutants. Biochemistry 2013; 52:8898-906. [PMID: 24261604 DOI: 10.1021/bi401330c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although CYP101D1 and P450cam catalyze the same reaction at similar rates and share strikingly similar active site architectures, there are significant functional differences. CYP101D1 thus provides an opportunity to probe what structural and functional features must be shared and what features can differ but maintain the high catalytic efficiency. Crystal structures of the cyanide complex of wild-type CYP101D1 and it active site mutants, D259N and T260A, have been determined. The conformational changes in CYP101D1 upon cyanide binding are very similar to those of P450cam, indicating a similar mechanism for proton delivery during oxygen activation using solvent-assisted proton transfer. The D259N-CN- complex shows a perturbed solvent structure compared to that of the wild type, which is similar to what was observed in the oxy complex of the corresonding D251N mutant in P450cam. As in P450cam, the T260A mutant is highly uncoupled while the D259N mutant gives barely detectable activity. Despite these similarities, CYP101D1 is able to use the P450cam redox partners while P450cam cannot use the CYP101D1 redox partners. Thus, the strict requirement of P450cam for its own redox partner is relaxed in CYP101D1. Differences in the local environment of the essential Asp (Asp259 in CYP101D1) provide a strucutral basis for understanding these functional differences.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697-3900, United States
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1338
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Nascimento AFZ, Trindade DM, Tonoli CCC, de Giuseppe PO, Assis LHP, Honorato RV, de Oliveira PSL, Mahajan P, Burgess-Brown NA, von Delft F, Larson RE, Murakami MT. Structural insights into functional overlapping and differentiation among myosin V motors. J Biol Chem 2013; 288:34131-34145. [PMID: 24097982 PMCID: PMC3837155 DOI: 10.1074/jbc.m113.507202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/27/2013] [Indexed: 11/06/2022] Open
Abstract
Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.
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Affiliation(s)
- Andrey F Z Nascimento
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Daniel M Trindade
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Priscila O de Giuseppe
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Leandro H P Assis
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Rodrigo V Honorato
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Paulo S L de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil
| | - Pravin Mahajan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Roy E Larson
- Department of Cellular & Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, São Paulo 14049-900, Brazil
| | - Mario T Murakami
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil.
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1339
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Liu Y, Olanrewaju YO, Zhang X, Cheng X. DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å. Biochemistry 2013; 52:9310-7. [PMID: 24236546 DOI: 10.1021/bi401360n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development. Zfp57 protein recognizes methylated CpG dinucleotide within GCGGCA elements at multiple imprinting control regions. In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic and van der Waals interactions. We examined the role of Glu182 in recognition of 5mC by mutagenesis. The majority of mutants examined lose selectivity of methylated (5mC) over unmodified (C) and oxidative derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC), suggesting that the side chain of Glu182 (the size and the charge) is dispensable for methyl group recognition but negatively impacts the binding of unmodified cytosine as well as oxidized derivatives of 5mC to achieve 5mC selectivity. Substitution of Glu182 with its corresponding amide (E182Q) had no effect on methylated DNA binding but gained significant binding affinity for 5caC DNA, resulting in a binding affinity for 5caC DNA comparable to that of the wild-type protein for 5mC. We show structurally that the uncharged amide group of E182Q interacts favorably with the carboxylate group of 5caC. Furthermore, introducing a positively charged arginine at position 182 resulted in a mutant (E182R) having higher selectivity for the negatively charged 5caC.
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Affiliation(s)
- Yiwei Liu
- Department of Biochemistry, Emory University School of Medicine , 1510 Clifton Road, Atlanta, Georgia 30322, United States
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1340
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Perkins A, Nelson KJ, Williams JR, Parsonage D, Poole LB, Karplus PA. The sensitive balance between the fully folded and locally unfolded conformations of a model peroxiredoxin. Biochemistry 2013; 52:8708-21. [PMID: 24175952 DOI: 10.1021/bi4011573] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To reduce peroxides, peroxiredoxins (Prxs) require a key "peroxidatic" Cys that, in a substrate-ready fully folded (FF) conformation, is oxidized to sulfenic acid and then, after a local unfolding (LU) of the active site, forms a disulfide bond with a second "resolving" Cys. For Salmonella typhimurium alkyl hydroperoxide reductase C (StAhpC) and some other Prxs, the FF structure is only known for a peroxidatic Cys→Ser variant, which may not accurately represent the wild-type enzyme. Here, we obtain the structure of authentic reduced wild-type StAhpC by dithiothreitol treatment of disulfide form crystals that fortuitously accommodate both the LU and FF conformations. The unique environment of one molecule in the crystal reveals a thermodynamic linkage between the folding of the active site loop and C-terminal regions, and comparisons with the Ser variant show structural and mobility differences from which we infer that the Cys→Ser mutation stabilizes the FF active site. A structure for the C165A variant (a resolving Cys to Ala mutant) in the same crystal form reveals that this mutation destabilizes the folding of the C-terminal region. These structures prove that subtle modifications to Prx structures can substantially influence enzymatic properties. We also present a simple thermodynamic framework for understanding the various mixtures of FF and LU conformations seen in these structures. On the basis of this framework, we rationalize how physiologically relevant regulatory post-translational modifications may modulate activity, and we propose a nonconventional strategy for designing selective Prx inhibitors.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
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1341
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Ahangar MS, Vyas R, Nasir N, Biswal BK. Structures of native, substrate-bound and inhibited forms of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2461-7. [PMID: 24311587 DOI: 10.1107/s0907444913022579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022]
Abstract
Imidazoleglycerol-phosphate dehydratase (IGPD; HisB), which catalyses the conversion of imidazoleglycerol-phosphate (IGP) to imidazoleacetol-phosphate in the histidine biosynthesis pathway, is absent in mammals. This feature makes it an attractive target for herbicide discovery. Here, the crystal structure of Mycobacterium tuberculosis (Mtb) IGPD is reported together with the first crystal structures of substrate-bound and inhibited (by 3-amino-1,2,4-triazole; ATZ) forms of IGPD from any organism. The overall tertiary structure of Mtb IGPD, a four-helix-bundle sandwiched between two four-stranded mixed β-sheets, resembles the three-dimensional structures of IPGD from other organisms; however, Mtb IGPD possesses a unique structural feature: the insertion of a one-turn 310-helix followed by a loop ten residues in length. The functional form of IGPD is 24-meric, exhibiting 432 point-group symmetry. The structure of the IGPD-IGP complex revealed that the imidazole ring of the IGP is firmly anchored between the two Mn atoms, that the rest of the substrate interacts through hydrogen bonds mainly with residues Glu21, Arg99, Glu180, Arg121 and Lys184 which protrude from three separate protomers and that the 24-mer assembly contains 24 catalytic centres. Both the structural and the kinetic data demonstrate that the inhibitor 3-amino-1,2,4-triazole inhibits IGPD competitively.
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Affiliation(s)
- Mohammad Syed Ahangar
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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1342
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Schacherl M, Waltersperger S, Baumann U. Structural characterization of the ribonuclease H-like type ASKHA superfamily kinase MK0840 from Methanopyrus kandleri. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2440-50. [PMID: 24311585 DOI: 10.1107/s0907444913022683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022]
Abstract
Murein recycling is a process in which microorganisms recover peptidoglycan-degradation products in order to utilize them in cell wall biosynthesis or basic metabolic pathways. Methanogens such as Methanopyrus kandleri contain pseudomurein, which differs from bacterial murein in its composition and branching. Here, four crystal structures of the putative sugar kinase MK0840 from M. kandleri in apo and nucleotide-bound states are reported. MK0840 shows high similarity to bacterial anhydro-N-acetylmuramic acid kinase, which is involved in murein recycling. The structure shares a common fold with panthothenate kinase and the 2-hydroxyglutaryl-CoA dehydratase component A, both of which are members of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases. Local conformational changes in the nucleotide-binding site between the apo and holo forms are observed upon nucleotide binding. Further insight is given into domain movements and putative active-site residues are identified.
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Affiliation(s)
- Magdalena Schacherl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, 50674 Cologne, Germany
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1343
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Benoit RM, Frey D, Hilbert M, Kevenaar JT, Wieser MM, Stirnimann CU, McMillan D, Ceska T, Lebon F, Jaussi R, Steinmetz MO, Schertler GFX, Hoogenraad CC, Capitani G, Kammerer RA. Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A. Nature 2013; 505:108-11. [PMID: 24240280 DOI: 10.1038/nature12732] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 10/03/2013] [Indexed: 01/09/2023]
Abstract
Botulinum neurotoxin A (BoNT/A) belongs to the most dangerous class of bioweapons. Despite this, BoNT/A is used to treat a wide range of common medical conditions such as migraines and a variety of ocular motility and movement disorders. BoNT/A is probably best known for its use as an antiwrinkle agent in cosmetic applications (including Botox and Dysport). BoNT/A application causes long-lasting flaccid paralysis of muscles through inhibiting the release of the neurotransmitter acetylcholine by cleaving synaptosomal-associated protein 25 (SNAP-25) within presynaptic nerve terminals. Two types of BoNT/A receptor have been identified, both of which are required for BoNT/A toxicity and are therefore likely to cooperate with each other: gangliosides and members of the synaptic vesicle glycoprotein 2 (SV2) family, which are putative transporter proteins that are predicted to have 12 transmembrane domains, associate with the receptor-binding domain of the toxin. Recently, fibroblast growth factor receptor 3 (FGFR3) has also been reported to be a potential BoNT/A receptor. In SV2 proteins, the BoNT/A-binding site has been mapped to the luminal domain, but the molecular details of the interaction between BoNT/A and SV2 are unknown. Here we determined the high-resolution crystal structure of the BoNT/A receptor-binding domain (BoNT/A-RBD) in complex with the SV2C luminal domain (SV2C-LD). SV2C-LD consists of a right-handed, quadrilateral β-helix that associates with BoNT/A-RBD mainly through backbone-to-backbone interactions at open β-strand edges, in a manner that resembles the inter-strand interactions in amyloid structures. Competition experiments identified a peptide that inhibits the formation of the complex. Our findings provide a strong platform for the development of novel antitoxin agents and for the rational design of BoNT/A variants with improved therapeutic properties.
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Affiliation(s)
- Roger M Benoit
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Daniel Frey
- 1] Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland [2]
| | - Manuel Hilbert
- 1] Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland [2]
| | - Josta T Kevenaar
- 1] Cell Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands [2]
| | - Mara M Wieser
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | | | - David McMillan
- UCB Celltech, UCB Pharma, UCB NewMedicines, Slough SL1 4EN, UK
| | - Tom Ceska
- UCB Celltech, UCB Pharma, UCB NewMedicines, Slough SL1 4EN, UK
| | - Florence Lebon
- UCB Pharma, UCB NewMedicines, B-1420 Braine-L'Alleud, Belgium
| | - Rolf Jaussi
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Gebhard F X Schertler
- 1] Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland [2] Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Casper C Hoogenraad
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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1344
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Halbach F, Reichelt P, Rode M, Conti E. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell 2013; 154:814-26. [PMID: 23953113 DOI: 10.1016/j.cell.2013.07.017] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 05/13/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S. cerevisiae 370 kDa core complex shows that Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. Biochemical data suggest that the Ski complex can thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Finally, we identify a Ski8-binding motif common to Ski3 and Spo11, rationalizing the moonlighting properties of Ski8 in mRNA decay and meiosis.
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Affiliation(s)
- Felix Halbach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany
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1345
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Grigg JC, Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 2013; 21:2025-32. [PMID: 24095061 PMCID: PMC3879790 DOI: 10.1016/j.str.2013.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 01/07/2023]
Abstract
T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. T box Stem I forms an arched conformation with extensive intermolecular contacts to two key points of tRNA, the anticodon and D/T-loops. Free and complexed tRNA exist in significantly different conformations, with the contacts stabilizing flexible D/T-loops and a rearrangement of the D-loop. Using a designed T box RNA/tRNA system, we demonstrate that the T box riboswitch monitors the length and orientation of two essential contacts. Length or orientation mismatches engineered into the T box riboswitch and tRNA disrupt the complex, whereas simultaneous insertion of full helical turns realigns the interfaces and restores interaction between artificially elongated T box riboswitch and tRNA molecules.
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Affiliation(s)
- Jason C. Grigg
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA,Correspondence:
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1346
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Hassan N, Tan TC, Spadiut O, Pisanelli I, Fusco L, Haltrich D, Peterbauer CK, Divne C. Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly. FEBS Open Bio 2013; 3:496-504. [PMID: 24282677 PMCID: PMC3839853 DOI: 10.1016/j.fob.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/17/2022] Open
Abstract
The flavin-dependent homotetrameric enzyme pyranose 2-oxidase (P2O) is found mostly, but not exclusively, in lignocellulose-degrading fungi where it catalyzes the oxidation of β-d-glucose to the corresponding 2-keto sugar concomitantly with hydrogen peroxide formation during lignin solubilization. Here, we present crystal structures of P2O from the efficient lignocellulolytic basidiomycete Phanerochaete chrysosporium. Structures were determined of wild-type PcP2O from the natural fungal source, and two variants of recombinant full-length PcP2O, both in complex with the slow substrate 3-deoxy-3-fluoro-β-d-glucose. The active sites in PcP2O and P2O from Trametes multicolor (TmP2O) are highly conserved with identical substrate binding. Our structural analysis suggests that the 17 °C higher melting temperature of PcP2O compared to TmP2O is due to an increased number of intersubunit salt bridges. The structure of recombinant PcP2O expressed with its natural N-terminal sequence, including a proposed propeptide segment, reveals that the first five residues of the propeptide intercalate at the interface between A and B subunits to form stabilizing, mainly hydrophobic, interactions. In the structure of mature PcP2O purified from the natural source, the propeptide segment in subunit A has been replaced by a nearby loop in the B subunit. We propose that the propeptide in subunit A stabilizes the A/B interface of essential dimers in the homotetramer and that, upon maturation, it is replaced by the loop in the B subunit to form the mature subunit interface. This would imply that the propeptide segment of PcP2O acts as an intramolecular chaperone for oligomerization at the A/B interface of the essential dimer. Structures of pyranose 2-oxidase from Phanerochaete chrysosporium were determined. The N-terminus may act as a propeptide with a role in homotetramer assembly. A large number of salt bridges between subunits provides thermostability. The substrate is bound in the productive binding mode for oxidation at C2.
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Key Words
- 2FGlc, 2-deoxy-2-fluoro-d-glucose
- 3FGlc, 3-deoxy-3-fluoro-d-glucose
- Crystal structure
- DTT, dithiothreitol
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- IMAC, by immobilized metal ion affinity chromatography
- IPTG, β-d-1-thiogalactopyranoside
- Lignin degradation
- MES, 2-(N-morpholino) ethanesulfonic acid
- MWCO, molecular weight cut off
- Oligomerization
- P2O, pyranose oxidase
- PBS, phosphate buffered saline
- PDB, Protein Data Bank
- PEG, polyethylene glycol
- Propeptide
- Pyranose 2-oxidase
- TEV, Tobacco Etch Virus
- Thermostability
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Affiliation(s)
- Noor Hassan
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Tien-Chye Tan
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
| | - Oliver Spadiut
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Ines Pisanelli
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Laura Fusco
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Dietmar Haltrich
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Clemens K. Peterbauer
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Christina Divne
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
- Corresponding author at: KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691StockholmSweden. Tel.: +46 8 55378296; fax: +46 8 55378468.
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1347
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Wan L, Zhang X, Williams SJ, Ve T, Bernoux M, Sohn KH, Jones JDG, Dodds PN, Kobe B. Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR-NB-LRR proteins that are involved in disease resistance in Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1275-80. [PMID: 24192368 PMCID: PMC3818052 DOI: 10.1107/s1744309113026614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 09/26/2013] [Indexed: 05/27/2023]
Abstract
The Toll/interleukin-1 receptor (TIR) domain is a protein-protein interaction domain that is found in both animal and plant immune receptors. The N-terminal TIR domain from the nucleotide-binding (NB)-leucine-rich repeat (LRR) class of plant disease-resistance (R) proteins has been shown to play an important role in defence signalling. Recently, the crystal structure of the TIR domain from flax R protein L6 was determined and this structure, combined with functional studies, demonstrated that TIR-domain homodimerization is a requirement for function of the R protein L6. To advance the molecular understanding of the function of TIR domains in R-protein signalling, the protein expression, purification, crystallization and X-ray diffraction analyses of the TIR domains of the Arabidopsis thaliana R proteins RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1) and the resistance-like protein SNC1 (suppressor of npr1-1, constitutive 1) are reported here. RPS4 and RRS1 function cooperatively as a dual resistance-protein system that prevents infection by three distinct pathogens. SNC1 is implicated in resistance pathways in Arabidopsis and is believed to be involved in transcriptional regulation through its interaction with the transcriptional corepressor TPR1 (Topless-related 1). The TIR domains of all three proteins have successfully been expressed and purified as soluble proteins in Escherichia coli. Plate-like crystals of the RPS4 TIR domain were obtained using PEG 3350 as a precipitant; they diffracted X-rays to 2.05 Å resolution, had the symmetry of space group P1 and analysis of the Matthews coefficient suggested that there were four molecules per asymmetric unit. Tetragonal crystals of the RRS1 TIR domain were obtained using ammonium sulfate as a precipitant; they diffracted X-rays to 1.75 Å resolution, had the symmetry of space group P4(1)2(1)2 or P4(3)2(1)2 and were most likely to contain one molecule per asymmetric unit. Crystals of the SNC1 TIR domain were obtained using PEG 3350 as a precipitant; they diffracted X-rays to 2.20 Å resolution and had the symmetry of space group P4(1)2(1)2 or P4(3)2(1)2, with two molecules predicted per asymmetric unit. These results provide a good foundation to advance the molecular and structural understanding of the function of the TIR domain in plant innate immunity.
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Affiliation(s)
- Li Wan
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoxiao Zhang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maud Bernoux
- CSIRO Plant Industry, Canberra, ACT 2601, Australia
| | - Kee Hoon Sohn
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, England
| | | | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
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1348
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Switching between the Alternative Structures and Functions of a 2-Cys Peroxiredoxin, by Site-Directed Mutagenesis. J Mol Biol 2013; 425:4556-68. [DOI: 10.1016/j.jmb.2013.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 12/28/2022]
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1349
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Williams LS, Levdikov VM, Minakhin L, Severinov K, Antson AA. 12-Fold symmetry of the putative portal protein from the Thermus thermophilus bacteriophage G20C determined by X-ray analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1239-41. [PMID: 24192358 PMCID: PMC3818042 DOI: 10.1107/s174430911302486x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/05/2013] [Indexed: 07/03/2024]
Abstract
In tailed bacteriophages and several animal viruses, the portal protein forms the gateway through which viral DNA is translocated into the head structure during viral particle assembly. In the mature virion the portal protein exists as a dodecamer, while recombinant portal proteins from several phages, including SPP1 and CNPH82, have been shown to form 13-subunit assemblies. A putative portal protein from the thermostable bacteriophage G20C has been cloned, overexpressed and purified. Crystals of the protein diffracted to 2.1 Å resolution and belonged to space group P42(1)2, with unit-cell parameters a = b = 155.3, c = 115.4 Å. The unit-cell content and self-rotation function calculations indicate that the protein forms a circular 12-subunit assembly.
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Affiliation(s)
- Lowri S. Williams
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Vladimir M. Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Leonid Minakhin
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- St Petersburg State Polytechnical University, St Petersburg 195251, Russian Federation
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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1350
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Vervaet N, Kallio JP, Meier S, Salmivaara E, Eberhardt M, Zhang S, Sun X, Wu Z, Kursula P, Kursula I. Recombinant production, crystallization and preliminary structural characterization of Schistosoma japonicum profilin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1264-7. [PMID: 24192365 PMCID: PMC3818049 DOI: 10.1107/s174430911302647x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 09/24/2013] [Indexed: 11/11/2022]
Abstract
Helminthic parasites of the genus Schistosoma contain a tegumental membrane, which is of crucial importance for modulation of the host immune response and parasite survival. The actin cytoskeleton plays an important role in the function of the tegument. Profilins are among the most important proteins regulating actin dynamics. Schistosoma japonicum possesses one profilin-like protein, which has been characterized as a potential vaccine candidate. Notably, profilins are highly immunogenic molecules in many organisms. Here, the profilin from S. japonicum was expressed, purified and crystallized. A native data set to 1.91 Å resolution and a single-wavelength anomalous diffraction (SAD) data set to a resolution of 2.2 Å were collected. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 31.82, b = 52.17, c = 59.79 Å and a = 35.29, b = 52.15, c = 59.82 Å, respectively.
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Affiliation(s)
- Nele Vervaet
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
| | - Juha Pekka Kallio
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
| | - Susanne Meier
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
| | - Emilia Salmivaara
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Maike Eberhardt
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Shuangmin Zhang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People’s Republic of China
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People’s Republic of China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People’s Republic of China
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Department of Chemistry, University of Hamburg, DESY, Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
| | - Inari Kursula
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Notkestrasse 85, Bldg. 25b, 22607 Hamburg, Germany
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
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