uu.seUppsala University Publications
Change search
Refine search result
1 - 14 of 14
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1. Andersson, Magnus
    et al.
    Malmerberg, Erik
    Westenhoff, Sebastian
    Katona, Gergely
    Cammarata, Marco
    Wohri, Annemarie B.
    Johansson, Linda C.
    Ewald, Friederike
    Eklund, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Wulff, Michael
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Neutze, Richard
    Structural Dynamics of Light-Driven Proton Pumps2009In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 17, no 9, p. 1265-1275Article in journal (Refereed)
    Abstract [en]

    Bacteriorhodopsin and proteorhodopsin are simple heptahelical proton pumps containing a retinal chromophore covalently bound to helix G via a protonated Schiff base. Following the absorption of a photon, all-trans retinal is isomerized to a 13-cis conformation, initiating a sequence of conformational changes driving vectorial proton transport. In this study we apply time-resolved wide-angle X-ray scattering to visualize in real time the helical motions associated with proton pumping by bacteriorhodopsin and proteorhodopsin. Our results establish that three conformational states are required to describe their photocycles. Significant motions of the cytoplasmic half of helix F and the extracellular half of helix C are observed prior to the primary proton transfer event, which increase in amplitude following proton transfer. These results both simplify the structural description to emerge from intermediate trapping studies of bacteriorhodopsin and reveal shared dynamical principles for proton pumping.

  • 2. Andersson, Magnus
    et al.
    Vincent, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Neutze, Richard
    A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins2008In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 16, no 1, p. 21-28Article in journal (Refereed)
    Abstract [en]

    Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.

  • 3. Di Yu, Xiao
    et al.
    Dubnovitsky, Anatoly
    Institutionen för molekylärbiologi - (slu).
    Pudney, Alex F.
    MacIntyre, Sheila
    Knight, Stefan D.
    Institutionen för molekylärbiologi - (slu) .
    Zavialov, Anton V.
    Institutionen för molekylärbiologi - (slu) .
    Allosteric Mechanism Controls Traffic in the Chaperone/Usher Pathway2012In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 20, no 11, p. 1861-1871Article in journal (Refereed)
    Abstract [en]

    Many virulence organelles of Gram-negative bacterial pathogens are assembled via the chaperone/usher pathway. The chaperone transports organelle subunits across the periplasm to the outer membrane usher, where they are released and incorporated into growing fibers. Here, we elucidate the mechanism of the usher-targeting step in assembly of the Yersinia pestis F1 capsule at the atomic level. The usher interacts almost exclusively with the chaperone in the chaperone:subunit complex. In free chaperone, a pair of conserved proline residues at the beginning of the subunit-binding loop form a "proline lock" that occludes the usher-binding surface and blocks usher binding. Binding of the subunit to the chaperone rotates the proline lock away from the usher-binding surface, allowing the chaperone-subunit complex to bind to the usher. We show that the proline lock exists in other chaperone/usher systems and represents a general allosteric mechanism for selective targeting of chaperone:subunit complexes to the usher and for release and recycling of the free chaperone.

  • 4.
    Dods, Robert
    et al.
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Båth, Petra
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Arnlund, David
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Beyerlein, Kenneth R.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Hamburg, Germany..
    Nelson, Garrett
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Liang, Mengling
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Harimoorthy, Rajiv
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Berntsen, Peter
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.;La Trobe Univ, Australian Res Council Ctr Excellence Adv Mol Ima, La Trobe Inst Mol Sci, Bundoora, Vic 3086, Australia..
    Malmerberg, Erik
    Lawrence Berkeley Natl Lab, Phys Biosci Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA..
    Johansson, Linda
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden.;Univ Southern Calif, Bridge Inst, Dept Chem, Los Angeles, CA 90089 USA..
    Andersson, Rebecka
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Bosman, Robert
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Carbajo, Sergio
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Claesson, Elin
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Conrad, Chelsie E.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Dahl, Peter
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Hammarin, Greger
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Hunter, Mark S.
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Li, Chufeng
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Lisova, Stella
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Milathianaki, Despina
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Robinson, Joseph
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Safari, Cecilia
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Sharma, Amit
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Williams, Garth
    Stanford Linear Accelerator Ctr SLAC Natl Acceler, Linac Coherent Light Source, Menlo Pk, CA USA..
    Wickstrand, Cecilia
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Yefanov, Oleksandr
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Hamburg, Germany..
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Hamburg, Germany..
    Barty, Anton
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Hamburg, Germany..
    Branden, Gisela
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    Neutze, Richard
    Univ Gothenburg, Dept Chem & Mol Biol, Gothenburg, Sweden..
    From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography2017In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 25, no 9, p. 1461-1468Article in journal (Refereed)
    Abstract [en]

    Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-angstrom to 2.4-angstrom resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.

  • 5.
    Fu, Ziao
    et al.
    Columbia Univ Coll Phys & Surg, Integrated Program Cellular Mol & Biomed Studies, 630 W 168th St, New York, NY 10032 USA..
    Kaledhonkar, Sandip
    Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10027 USA..
    Borg, Anneli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Sun, Ming
    Columbia Univ, Dept Biol Sci, New York, NY 10027 USA..
    Chen, Bo
    Columbia Univ, Dept Biol Sci, New York, NY 10027 USA..
    Grassucci, Robert A.
    Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10027 USA.;Columbia Univ, Howard Hughes Med Inst, New York, NY 10032 USA..
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Frank, Joachim
    Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10027 USA.;Columbia Univ, Dept Biol Sci, New York, NY 10027 USA.;Columbia Univ, Howard Hughes Med Inst, New York, NY 10032 USA..
    Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryoelectron Microscopy2016In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 24, no 12, p. 2092-2101Article in journal (Refereed)
    Abstract [en]

    Upon encountering a stop codon on mRNA, polypeptide synthesis on the ribosome is terminated by release factors, and the ribosome complex, still bound with mRNA and P-site-bound tRNA (post-termination complex, PostTC), is split into ribosomal subunits, ready for a new round of translational initiation. Separation of post-termination ribosomes into subunits, or "ribosome recycling,'' is promoted by the joint action of ribosome-recycling factor (RRF) and elongation factor G (EF-G) in a guanosine triphosphate (GTP) hydrolysis-dependent manner. Here we used a mixing-spraying-based method of time-resolved cryo-electron microscopy (cryo-EM) to visualize the short-lived intermediates of the recycling process. The two complexes that contain (1) both RRF and EF-G bound to the PostTC or (2) deacylated tRNA bound to the 30S subunit are of particular interest. Our observations of the native form of these complexes demonstrate the strong potential of time-resolved cryo-EM for visualizing previously unobservable transient structures.

  • 6. Gan, Lu
    et al.
    Speir, Jeffrey A.
    Conway, James F.
    Lander, Gabriel
    Cheng, Naiqian
    Firek, Brian A.
    Hendrix, Roger W.
    Duda, Robert L.
    Liljas, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
    Johnson, John E.
    Capsid Conformational Sampling in HK97 Maturation Visualized by X-Ray Crystallography and Cryo-EM2006In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 14, no 11, p. 1655-1665Article in journal (Refereed)
    Abstract [en]

    Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 angstrom radial expansion. The mature particle is formed by 420 copies of the major capsid protein organized on a T = 7 laevo, lattice with each subunit covalently crosslinked to two neighbors. Well-characterized pH 4 expansion intermediates make HK97 valuable for investigating quaternary structural dynamics. Here, we use X-ray crystallography and cryo-EM to demonstrate that in the final transition in maturation (requiring neutral pH), pentons in Expansion Intermediate IV (EI-IV) reversibly sample 14 angstrom translations and 6 degrees rotations relative to a fixed hexon lattice. The limit of this trajectory corresponds to the Head II conformation that is secured at this extent only by the formation of the final class of covalent crosslinks. Mutants that cannot crosslink or EI-IV particles that have been rendered incapable of forming the final crosslink remain in the EI-IV state.

  • 7. Gianni, Stefano
    et al.
    Walma, Tine
    Arcovito, Alessandro
    Calosci, Nicoletta
    Bellelli, Andrea
    Engström, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Travaglini-Allocatelli, Carlo
    Brunori, Maurizio
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Vuister, Geerten W.
    Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering2006In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 14, no 12, p. 1801-1809Article in journal (Refereed)
    Abstract [en]

    Understanding the basis of communication within protein domains is a major challenge in structural biology. We present structural and dynamical evidence for allosteric effects in a PDZ domain, PDZ2 from the tyrosine phosphatase PTP-BL, upon binding to a target peptide. The NMR structures of its free and peptide-bound states differ in the orientation of helix alpha 2 with respect to the remainder of the molecule, concomitant with a readjustment of the hydrophobic core. Using an ultrafast mixing instrument, we detected a deviation from simple bimolecular kinetics for the association with peptide that is consistent with a rate-limiting conformational change in the protein (k(obs) similar to 7 x 10(3) s(-1)) and an induced-fit model. Furthermore, the binding kinetics of 15 mutants revealed that binding is regulated by long-range interactions, which can be correlated with the structural rearrangements resulting from peptide binding. The homologous protein PSD-95 PDZ3 did not display a similar ligand-induced conformational change.

  • 8.
    Gutlerrez-de-Teran, Hugo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Massink, Arnault
    Rodriguez, David
    Liu, Wei
    Han, Gye Won
    Joseph, Jeremiah S.
    Katritch, Ilia
    Heitman, Laura H.
    Xia, Lizi
    IJzerman, Adriaan P.
    Cherezov, Vadim
    Katritch, Vsevolod
    Stevens, Raymond C.
    The Role of a Sodium Ion Binding Site in the Allosteric Modulation of the A(2A) Adenosine G Protein-Coupled Receptor2013In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 21, no 12, p. 2175-2185Article in journal (Refereed)
    Abstract [en]

    The function of G protein-coupled receptors (GPCRs) can be modulated by a number of endogenous allosteric molecules. In this study, we used molecular dynamics, radioligand binding, and thermostability experiments to elucidate the role of the recently discovered sodium ion binding site in the allosteric modulation of the human A(2A) adenosine receptor, conserved among class A GPCRs. While the binding of antagonists and sodium ions to the receptor was noncompetitive in nature, the binding of agonists and sodium ions appears to require mutually exclusive conformational states of the receptor. Anniloride analogs can also bind to the sodium binding pocket, showing distinct patterns of agonist and antagonist modulation. These findings suggest that physiological concentrations of sodium ions affect functionally relevant conformational states of GPCRs and can help to design novel synthetic allosteric modulators or bitopic ligands exploiting the sodium ion binding pocket.

  • 9.
    Hultqvist, Greta
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Haq, Raza
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Punekar, Avinash
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Chi, Celestine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. ETH.
    Engström, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bach, Anders
    Strømgaard, Kristian
    University of Copenhagen.
    Selmer, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Gianni, Stefano
    Sapienza Università di Roma.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Energetic pathway sampling in a protein interaction domain2013In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 21, p. 1193-1202Article in journal (Other academic)
    Abstract [en]

    The affinity and specificity of protein-ligand interactions are influenced by energeticcrosstalk within the protein domain. However, the molecular details of such intradomain allostery are still unclear. Here, we have experimentally detected and computationally predicted interactionpathways in the postsynaptic density 95/discs large/zonula occludens 1 (PDZ)-peptide ligand model system using wild-type and circularly permuted PDZ proteins. The circular permutant introduced small perturbations in the tertiary structure and a concomitant rewiring of allosteric pathways, allowing us to describe how subtle changes may reshape energetic signaling. The results were analyzed in the context of other members of the PDZ family, which were found to contain distinct interaction pathways for different peptide ligands. The data reveal a fascinating scenario whereby several energetic pathways are sampled within one single domain and distinct pathways are activated by specific protein ligands. 

  • 10. Marklund, Erik G
    et al.
    Degiacomi, Matteo T
    Robinson, Carol V
    Baldwin, Andrew J
    Benesch, Justin L P
    Collision cross sections for structural proteomics.2015In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 23, no 4Article in journal (Refereed)
    Abstract [en]

    Ion mobility mass spectrometry (IM-MS) allows the structural interrogation of biomolecules by reporting their collision cross sections (CCSs). The major bottleneck for exploiting IM-MS in structural proteomics lies in the lack of speed at which structures and models can be related to experimental data. Here we present IMPACT (Ion Mobility Projection Approximation Calculation Tool), which overcomes these twin challenges, providing accurate CCSs up to 10(6) times faster than alternative methods. This allows us to assess the CCS space presented by the entire structural proteome, interrogate ensembles of protein conformers, and monitor molecular dynamics trajectories. Our data demonstrate that the CCS is a highly informative parameter and that IM-MS is of considerable practical value to structural biologists.

  • 11. Read, Randy J.
    et al.
    Adams, Paul D.
    Arendall, W. Bryan, III
    Brunger, Axel T.
    Emsley, Paul
    Joosten, Robbie P.
    Kleywegt, Gerard J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Krissinel, Eugene B.
    Luetteke, Thomas
    Otwinowski, Zbyszek
    Perrakis, Anastassis
    Richardson, Jane S.
    Sheffler, William H.
    Smith, Janet L.
    Tickle, Ian J.
    Vriend, Gert
    Zwart, Peter H.
    A New Generation of Crystallographic Validation Tools for the Protein Data Bank2011In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 19, no 10, p. 1395-1412Article in journal (Refereed)
    Abstract [en]

    This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a now assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

  • 12.
    Selmer, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
    Liljas, Anders
    Exit biology: battle for the nascent chain2008In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 16, no 4, p. 498-500Article, review/survey (Other academic)
  • 13. Wu, Mousheng
    et al.
    Nilsson, Per
    Henriksson, Niklas
    Niedzwiecka, Anna
    Lim, Meng Kiat
    Cheng, Zhihong
    Kokkoris, Kyriakos
    Virtanen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Song, Haiwei
    Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease2009In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 17, no 2, p. 276-286Article in journal (Refereed)
    Abstract [en]

    Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveals that, in one subunit, m(7)GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it binds almost exclusively to the RRM domain. Importantly, our structural and competition data show that the cap-binding site overlaps with the active site in the nuclease domain. Mutational analysis demonstrates that residues involved in m(7)G recognition are crucial for cap-stimulated deadenylation activity, and those involved in both cap and poly(A) binding are important for catalysis. A modeled PARN, which shows that the RRM domain from one subunit and the R3H domain from the other subunit enclose the active site, provides a structural foundation for further studies to elucidate the mechanism of PARN-mediated deadenylation.

  • 14. Zhang, Rong guang
    et al.
    Andersson, C Evalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Savchenko, Alexei
    Skarina, Tatiana
    Evdokimova, Elena
    Beasley, Steven
    Arrowsmith, Cheryl H
    Edwards, Aled M
    Joachimiak, Andrzej
    Mowbray, Sherry L
    Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle2003In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 11, no 1, p. 31-42Article in journal (Refereed)
    Abstract [en]

    Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from Escherichia coli was solved by multiwavelength anomalous diffraction (MAD) phasing, and refined to 1.5 A resolution (R factor 22.4%, R(free) 23.7%). RpiA exhibits an alpha/beta/(alpha/beta)/beta/alpha fold, some portions of which are similar to proteins of the alcohol dehydrogenase family. The two subunits of the dimer in the asymmetric unit have different conformations, representing the opening/closing of a cleft. Active site residues were identified in the cleft using sequence conservation, as well as the structure of a complex with the inhibitor arabinose-5-phosphate at 1.25 A resolution. A mechanism for acid-base catalysis is proposed.

1 - 14 of 14
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf