DOCSLIB.ORG

ATP Synthase from Trypanosoma Brucei Has an Elaborated Canonical F1-Domain and Conventional Catalytic Sites

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
ATP Synthase from Trypanosoma Brucei Has an Elaborated Canonical F1-Domain and Conventional Catalytic Sites ATP synthase from Trypanosoma brucei has an elaborated canonical F1-domain and conventional catalytic sites Martin G. Montgomerya,1, Ondrej Gahuraa,b,1, Andrew G. W. Lesliec, Alena Zíkováb, and John E. Walkera,2 aThe Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceské Budejovice, Czech Republic; and cThe Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom Contributed by John E. Walker, December 18, 2017 (sent for review December 1, 2017; reviewed by Thomas M. Duncan and Wayne D. Frasch) The structures and functions of the components of ATP synthases, and penetrates into the α3β3-domain, where the catalytic sites of especially those subunits involved directly in the catalytic forma- the enzyme are found at three of the interfaces of α- and tion of ATP, are widely conserved in metazoans, fungi, eubacteria, β-subunits. The penetrant region of the central stalk is an and plant chloroplasts. On the basis of a map at 32.5-Å resolution asymmetric α-helical coiled coil, and its rotation inside the α3β3- determined in situ in the mitochondria of Trypanosoma brucei by domain takes each catalytic site through a series of conforma- electron cryotomography, it has been proposed that the ATP syn- tional changes that lead to the binding of substrates and the thase in this species has a noncanonical structure and different formation and release of ATP. catalytic sites in which the catalytically essential arginine finger During ATP hydrolysis in the experimentally detached F1- is provided not by the α-subunit adjacent to the catalytic domain, the direction of rotation, now driven by energy released nucleotide-binding site as in all species investigated to date, but from the hydrolysis of ATP, is opposite to the synthetic sense. rather by a protein, p18, found only in the euglenozoa. A crystal Extensive structural analyses, mostly by X-ray crystallography at structure at 3.2-Å resolution of the catalytic domain of the same atomic resolution, have shown that the F1-domains of the en- enzyme demonstrates that this proposal is incorrect. In many re- zymes from bovine (3–23) and yeast (24–30) mitochondria, spects, the structure is similar to the structures of F1-ATPases de- chloroplasts (31, 32), and eubacteria (33–39) are highly con- α β termined previously. The 3 3-spherical portion of the catalytic served. Not only is there conservation of the subunit composi- domain in which the three catalytic sites are found, plus the cen- tions of the α3β3-domain and the central stalk (γ1e1 in eubacteria tral stalk, are highly conserved, and the arginine finger is provided γ δ α and chloroplasts, and 1 1 plus an additional unique subunit, conventionally by the -subunits adjacent to each of the three confusingly called e, attached to the δ-subunit in mitochondria catalytic sites found in the β-subunits. Thus, the enzyme has a orthologs), but also the sequences of subunits are either highly conventional catalytic mechanism. The structure differs from pre- conserved or absolutely conserved in many key residues. This vious described structures by the presence of a p18 subunit, iden- extensive conservation includes residues in catalytic interfaces tified only in the euglenozoa, associated with the external surface and in the catalytic sites themselves. In the β-subunits, they of each of the three α-subunits, thereby elaborating the F1-domain. Subunit p18 is a pentatricopeptide repeat (PPR) protein with three PPRs and appears to have no function in the catalytic Significance mechanism of the enzyme. Mitochondria generate the cellular fuel ATP to sustain complex ATP synthase | Trypanosoma brucei | p18 subunit | catalytic domain | structure life. Production of ATP depends on the oxidation of energy-rich compounds to produce the proton motive force (pmf), a chemical potential difference for protons, across the inner he ATP synthases, also known as F-ATPases or F1Fo- TATPases, are multisubunit enzyme complexes found in membrane. The pmf drives the ATP synthase to synthesize ATP energy-transducing membranes in eubacteria, chloroplasts, and via a mechanical rotary mechanism. The structures and func- mitochondria (1, 2). They make ATP from ADP and phosphate tions of the protein components of this molecular machine, under aerobic conditions using a proton-motive force (pmf), especially those involved directly in the catalytic formation of generated by respiration or photosynthesis, as a source of energy. ATP, are widely conserved in metazoans, fungi, and eubacteria. Here we show that the proposal that this conservation does To date, studies of the subunit compositions, structures, and Trypanosoma brucei mechanism of the ATP synthases have been confined mainly to not extend to the ATP synthase from ,a member of the euglenozoa and the causative agent of sleeping the vertebrates, especially humans and bovines, and to various sickness in humans, is incorrect. fungi, eubacteria, and chloroplasts of green plants. These studies have established the conservation of the central features of these Author contributions: A.Z. and J.E.W. designed research; M.G.M. and O.G. performed rotary machines. They are all membrane-bound assemblies of research; M.G.M., A.G.W.L., and J.E.W. analyzed data; J.E.W. wrote the paper; and multiple subunits organized into membrane-intrinsic and J.E.W. supervised the project. membrane-extrinsic sectors. Reviewers: T.M.D., State University of New York Upstate Medical University; and W.D.F., Arizona State University. The membrane-extrinsic sector, known as F1-ATPase, is the catalytic part in which ATP is formed from ADP and inorganic The authors declare no conflict of interest. phosphate. It can be detached experimentally from the mem- Published under the PNAS license. brane domain in an intact state, and retains the ability to hy- Data deposition: The atomic coordinates and structure factors have been deposited in the drolyze, but not synthesize, ATP. The membrane intrinsic sector, Protein Data Bank, www.wwpdb.org (PDB ID code 6F5D). 1 sometimes called Fo, contains a rotary motor driven by pmf and M.G.M. and O.G. contributed equally to this work. is connected to the extrinsic domain by a central stalk and a 2To whom correspondence should be addressed. Email: [email protected]. peripheral stalk. The enzyme’s rotor constitutes the central stalk This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. and an associated ring of c-subunits in the membrane domain. 1073/pnas.1720940115/-/DCSupplemental. The central stalk lies along an axis of sixfold pseudosymmetry Published online February 12, 2018. 2102–2107 | PNAS | February 27, 2018 | vol. 115 | no. 9 www.pnas.org/cgi/doi/10.1073/pnas.1720940115 Downloaded by guest on September 24, 2021 include a hydrophobic pocket where the adenine ring of ADP (or crystallized in the presence of phosphonate (20) and in the α β ATP) is bound; a P-loop sequence that interacts with the -, -, F1-ATPase from Caldalkalibacillus thermarum (38). These struc- and γ-phosphates of ATP and provides residues involved either tures are interpreted as representing a posthydrolysis state in directly or indirectly via water molecules in the binding of a hexa- which the ADP molecule has not been released from the coordinate magnesium ion; and, in the adjacent α-subunit, an enzyme. “ ” arginine finger residue, which senses whether ADP or ATP is An unusual feature of the T. brucei F1-ATPase is that the bound to the catalytic site. Indeed, these catalytic features are diphosphate catalytic interface is more open than the tri- common to a wide range of NTPases (40, 41), and together with phosphate catalytic interface, similar to the F1-ATPase from conserved structural features are characteristic of the canonical Saccharomyces cerevisiae (24), whereas the converse is observed ATP synthase. in all other structures (Table S2). As usual, the empty interface is Based on a structural model at 32.5-Å resolution derived by the most open of the three catalytic interfaces (Table S2). The electron cryotomography (ECT), it has been suggested recently rotational position of the γ-subunit (determined by superposition that the structure of the F1-catalytic domain and its catalytic of crown regions of structures) is +23.1° relative to the bovine Trypanosoma brucei mechanism in the ATP synthase from have phosphate release dwell, which is at or close to the catalytic dwell diverged extensively from the canonical complex in an un- at +30° in the rotary catalytic cycle (6). precedented manner (42). It has been proposed that the struc- ture of this F1-domain is much more open than those described Structure of the F1-ATPase from T. brucei. The structure consists of “ ” in other species, and that the arginine finger is provided not by an α β -complex with α- and β-subunits arranged in alternation α 3 3 the -subunit, but rather by an additional p18-subunit found only around an antiparallel α-helical coiled coil in the γ-subunit (Fig. in the euglenozoa (43–49). Here we examine this proposal in γ α β T. brucei 1). The rest of the -subunit sits beneath the 3 3-complex and is the context of a structure of the F1-domain of the associated with the δ- and e-subunits. Together, these three ATP synthase determined by X-ray crystallography at 3.2- subunits form the central stalk. Thus, the overall structure of this Å resolution. catalytic domain of the ATP synthase complex is very close to Results and Discussion structures of canonical F1-ATPases determined in the mito- chondria of other species, and in eubacteria and chloroplasts. Structure Determination. The crystals of the T.
Load more

Recommended publications
  • Crystal Structure of the Bloom's Syndrome Helicase Indicates a Role
    Nucleic Acids Research Advance Access published April 21, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv373 Crystal structure of the Bloom’s syndrome helicase indicates a role for the HRDC domain in conformational changes Joseph A. Newman1,†, Pavel Savitsky1,†, Charles K. Allerston1, Anna H. Bizard2, Ozg¨ un¨ Ozer¨ 2, Kata Sarlos´ 2, Ying Liu2, Els Pardon3,4, Jan Steyaert3,4, Ian D. Hickson2 and Opher Gileadi1,* 1Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK, 2Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark, 3Structural Biology Downloaded from Brussels, Vrije Universiteit Brussel, Pleinlaan 2 , 1050 Brussels, Belgium and 4Structural Biology Research Center, VIB, Brussel, Pleinlaan 2, 1050 Brussels, Belgium Received January 13, 2015; Revised March 27, 2015; Accepted April 03, 2015 http://nar.oxfordjournals.org/ ABSTRACT some instability, including chromatid gaps and breaks (4), various chromosome structural rearrangements (5)andan Bloom’s syndrome helicase (BLM) is a member of the increase in the number of sister chromatid exchange (SCE) RecQ family of DNA helicases, which play key roles in events, the latter serving as a distinguishing feature for the the maintenance of genome integrity in all organism clinical diagnosis of BS (6). groups. We describe crystal structures of the BLM Bloom’s syndrome helicase (BLM), like all RecQ-family helicase domain in complex with DNA and with an an- helicases, acts as a 3 to 5 helicase (7) on a wide variety tibody fragment, as well as SAXS and domain asso- of DNA substrates including forked duplexes, G quadru- at Chadwick & RAL Libraries on April 23, 2015 ciation studies in solution.
    [Show full text]
  • Neurofibromin Controls Macropinocytosis and Phagocytosis
    RESEARCH ARTICLE elifesciences.org Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium Gareth Bloomfield1*, David Traynor1, Sophia P Sander1,2, Douwe M Veltman1, Justin A Pachebat3,4, Robert R Kay1 1MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; 2Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, United Kingdom; 3Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom; 4Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom Abstract Cells use phagocytosis and macropinocytosis to internalise bulk material, which in phagotrophic organisms supplies the nutrients necessary for growth. Wildtype Dictyostelium amoebae feed on bacteria, but for decades laboratory work has relied on axenic mutants that can also grow on liquid media. We used forward genetics to identify the causative gene underlying this phenotype. This gene encodes the RasGAP Neurofibromin (NF1). Loss of NF1 enables axenic growth by increasing fluid uptake. Mutants form outsized macropinosomes which are promoted by greater Ras and PI3K activity at sites of endocytosis. Relatedly, NF1 mutants can ingest larger-than-normal particles using phagocytosis. An NF1 reporter is recruited to nascent macropinosomes, suggesting that NF1 limits their size by locally inhibiting Ras signalling. Our results link NF1 with macropinocytosis and phagocytosis for the first time, and we propose that NF1 evolved in early phagotrophs to spatially modulate Ras activity, thereby constraining and shaping their feeding structures. DOI: 10.7554/eLife.04940.001 *For correspondence: garethb@ mrc-lmb.cam.ac.uk Introduction Phagotrophic cells feed by performing large-scale endocytosis. A wide range of unicellular Competing interests: The eukaryotes grow in this way, suggesting that it is extremely old in evolutionary terms (Stanier, authors declare that no 1970; Cavalier-Smith, 2002; Yutin et al., 2009).
    [Show full text]
  • Molecular Switch-Like Regulation Enables Global Subunit Coordination in a Viral Ring Atpase
    Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase Sara Tafoyaa,b,c, Shixin Liud, Juan P. Castilloa,b, Rockney Atze,f, Marc C. Moraisg, Shelley Grimese,f,1, Paul J. Jardinee,f, and Carlos Bustamantea,b,c,h,i,j,k,l,2 aJason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, CA 94720; bHoward Hughes Medical Institute, University of California, Berkeley, CA 94720; cBiophysics Graduate Group, University of California, Berkeley, CA 94720; dLaboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065; eInstitute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455; fDepartment of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455; gSealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555; hDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; iDepartment of Physics, University of California, Berkeley, CA 94720; jDepartment of Chemistry, University of California, Berkeley, CA 94720; kCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and lKavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720 Edited by Ken A. Dill, Stony Brook University, Stony Brook, NY, and approved June 15, 2018 (received for review February 20, 2018) Subunits in multimeric ring-shaped motors must coordinate their the φ29 ring ATPase can be thought of as five molecular switches activities to ensure correct and efficient performance of their arranged in a closed configuration. Moreover, the enzymatic activity mechanical tasks. Here, we study WT and arginine finger mutants of one of the subunits is up-regulated compared with the other four, of the pentameric bacteriophage φ29 DNA packaging motor.
    [Show full text]
  • The Molecular Coupling Between Substrate Recognition and ATP Turnover in A
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader Neha Puri1,2, Amy J. Fernandez1, Valerie L. O’Shea Murray1,3, Sarah McMillan4, James L. Keck4, James M. Berger1,* 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205 2Bristol Myers Squibb, 38 Jackson Road, Devens, MA 01434 3Saul Ewing Arnstein & Lehr, LLP, Centre Square West, 1500 Market Street, 38th Floor, Philadelphia, PA 19102 4Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706 *Corresponding author Email: [email protected] Keywords: DNA replication, AAA+ ATPase, Helicase, Meier-Gorlin Syndrome 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.21.345918; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT In many bacteria and in eukaryotes, replication fork establishment requires the controlled loading of hexameric, ring-shaped helicases around DNA by AAA+ ATPases. How loading factors use ATP to control helicase deposition is poorly understood.
    [Show full text]
  • The GAP Arginine Finger Movement Into the Catalytic Site of Ras Increases the Activation Entropy
    The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy Carsten Ko¨ tting†, Angela Kallenbach†, Yan Suveyzdis†, Alfred Wittinghofer‡, and Klaus Gerwert†§ †Lehrstuhl fu¨r Biophysik, Ruhr-Universita¨t Bochum, D-44780 Bochum, Germany; and ‡Max-Planck-Institut fu¨r Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany Edited by Robert H. Austin, Princeton University, Princeton, NJ, and approved February 14, 2008 (received for review December 28, 2007) Members of the Ras superfamily of small G proteins play key roles the GAP-mediated catalysis as a prerequisite for a rational drug in signal transduction pathways, which they control by GTP hy- development (8). drolysis. They are regulated by GTPase activating proteins (GAPs). The key residue for GAP-mediated catalysis is the so-called Mutations that prevent hydrolysis cause severe diseases including ‘‘arginine finger’’ (9). In the x-ray structure of the Ras⅐GDP⅐ cancer. A highly conserved ‘‘arginine finger’’ of GAP is a key AlF3⅐RasGAP complex mimicking the transition state, it points residue. Here, we monitor the GTPase reaction of the Ras⅐RasGAP into the GTP binding site of Ras. It stabilizes the position of the complex at high temporal and spatial resolution by time-resolved catalytic Gln-61 and neutralizes negative charge on the phos- FTIR spectroscopy at 260 K. After triggering the reaction, we phates (10). The catalytic arginine finger is a highly conserved observe as the first step a movement of the switch-I region of Ras motive among several GAP proteins for small G proteins (11). from the nonsignaling ‘‘off’’ to the signaling ‘‘on’’ state with a rate The participation of an arginine in phosphoryl transfer as seen of3s؊1.
    [Show full text]
  • Role of the Arginine Finger in Ras-Rasgap Revealed by QM/MM Calculations
    Role of the arginine finger in Ras-RasGAP revealed by QM/MM calculations Henrik te Heesen, Klaus Gerwert, and Jürgen Schlitter Department of Biophysics, ND 04, University of Bochum, 44801 Bochum, Germany. Mail: [email protected] Ras is a key enzyme in cellular signal transduction inducing cell division. The signal is ON when Ras contains the substrate guanosine triphosphate (GTP). The OFF state is taken during hydrolysis of GTP to GDP and Pi. The switch is induced by the activator RasGAP docking to Ras. In the Ras-RasGAP complex, hydrolysis of GTP is strongly accelerated as compared to Ras alone (105 times). This is largely attributed to the arginine finger R789 of RasGAP pointing to the tip of the substrate in the transition state analogue (1). We performed QM/MM simulations where triphosphate was treated using density functional theory while the protein complex and water environment were described classically using MD. IR spectra of triphosphate and various properties were calculated for Ras and Ras-RasGAP. Compared to Ras, charge shift, bond stretching and distortion towards an eclipsed γ-to-β orientation are much more pronounced in the complex. The crucial electron shift is such that GTP approaches the charge distribution of the product state. The explanation is found by detailed analysis of the electrostatic field at the phosphorus atoms. The positive charge of the arginine finger has a negligible or even counterproductive effect. Instead, arginine is shown to act by displacing water (~ 14 molecules) out of the binding niche. The resulting enhanced electrostatic field catalyses the cleavage step (2).
    [Show full text]
  • Microorganisms
    microorganisms Review Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes Adam Kawalek y , Pawel Wawrzyniak y, Aneta Agnieszka Bartosik and Grazyna Jagura-Burdzy * Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi´nskiego5a, 02-106 Warsaw, Poland; [email protected] (A.K.); [email protected] (P.W.); [email protected] (A.A.B.) * Correspondence: [email protected]; Tel.: +48-225921212 These authors contributed equally to this work. y Received: 4 December 2019; Accepted: 9 January 2020; Published: 11 January 2020 Abstract: The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins.
    [Show full text]
  • Arginine Finger Regulates Sequential Action of Asymmetrical Hexameric
    MCB Accepted Manuscript Posted Online 25 July 2016 Mol. Cell. Biol. doi:10.1128/MCB.00142-16 Copyright © 2016 Zhao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. 1 Arginine finger regulates sequential action of asymmetrical 2 hexameric ATPase in dsDNA translocation motor 3 Downloaded from 4 Zhengyi Zhao, 1,2 Gian Marco De-Donatis, 2 Chad Schwartz, 2 Huaming Fang, 2 Jingyuan Li,3 and 5 Peixuan Guo1,2 * 6 1 7 College of Pharmacy, Department of Physiology & Cell Biology/College of Medicine, and http://mcb.asm.org/ 8 Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 9 USA 10 2Nanobiotechnology Center, Department of Pharmaceutical Sciences, College of Pharmacy, 11 Markey Cancer Center, University of Kentucky, Lexington, KY, USA on August 9, 2016 by Ohio State University 12 3CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center 13 for Nanoscience and Technology of China and Institute of High Energy Physics, Beijing, China 14 15 Running Title: Arginine finger primes sequential action of ATPase 16 17 *Address correspondence to: 18 Peixuan Guo, Ph.D. 19 Sylvan G. Frank Endowed Chair in Pharmaceutics and Drug Delivery System, College of 20 Pharmacy, and Department of Physiology and Cell Biology/College of Medicine, 21 Ohio State University, Hamilton Hall, 1645 Neil Ave, Columbus, Ohio, 43210, USA 22 Email: [email protected] 23 Phone: (614)-293-2114 (office) 1 24 ABSTRACT 25 Biological motors are ubiquitous in living systems. Currently, how the motor component 26 coordinates the unidirectional motion is elusive in most cases.
    [Show full text]
  • The Arginine Finger of Bacteriophage T7 Gene 4 Helicase: Role in Energy Coupling
    The arginine finger of bacteriophage T7 gene 4 helicase: Role in energy coupling Donald J. Crampton, Shenyuan Guo*, Donald E. Johnson, and Charles C. Richardson† Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Contributed by Charles C. Richardson, February 10, 2004 The DNA helicase encoded by gene 4 of bacteriophage T7 couples subsequently identified in other NTP-hydrolyzing enzymes such DNA unwinding to the hydrolysis of dTTP. The loss of coupling in as the F1-ATPase (19). the presence of orthovanadate (Vi) suggests that the ␥-phosphate An arginine finger is recognized as an arginine residue that of dTTP plays an important role in this mechanism. The crystal coordinates the ␥-phosphate of a bound nucleotide, with the structure of the hexameric helicase shows Arg-522, located at the arginine residue being located distal to the nucleotide-binding subunit interface, positioned to interact with the ␥-phosphate of site. The arginine can reside on a distinct activator protein, as in bound nucleoside 5؅ triphosphate. In this respect, it is analogous to the case of GAP-Ras (20, 21), an adjacent subunit of an arginine fingers found in other nucleotide-hydrolyzing enzymes. oligomeric protein such as the F1-ATPase (17), or a distinct When Arg-522 is replaced with alanine (gp4-R522A) or lysine domain within the protein itself (22). Arginine fingers contribute (gp4-R522K), the rate of dTTP hydrolysis is significantly decreased. to NTP hydrolysis through stabilization of the transition state of dTTPase activity of the altered proteins is not inhibited by Vi, the reaction and as a trigger for conformational changes after suggesting the loss of an interaction between Vi and gene 4 hydrolysis of dTTP (19, 23, 24).
    [Show full text]
  • Aspects Moléculaires Des Hélicases De La Famille De Recq Hua Ren
    Aspects moléculaires des hélicases de la famille de RecQ Hua Ren To cite this version: Hua Ren. Aspects moléculaires des hélicases de la famille de RecQ. Sciences du Vivant [q-bio]. École normale supérieure de Cachan - ENS Cachan, 2009. Français. tel-00448084 HAL Id: tel-00448084 https://tel.archives-ouvertes.fr/tel-00448084 Submitted on 18 Jan 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE DE DOCTORAT DE L’ECOLE NORMALE SUPERIEURE DE CACHAN Présentée par Madame Hua REN pour obtenir le grade de DOCTEUR DE L’ECOLE NORMALE SUPERIEURE DE CACHAN Domaine : SCIENCES DE LA VIE ET DE LA SANTE Sujet de la thèse: Aspects moléculaires des hélicases de la famille de RecQ Thèse présentée et soutenue à ECNU Chine le 28 / 09/ 2009 devant le jury composé de : M. Marc BOUDVILLAIN Président/Rapporteur M. Jie-min WENG Rapporteur M. Duan MA Examinateur Mme Min QIAN Co-Directrice de thèse M. Xu-guang XI Co-Directeur de thèse Nom du Laboratoire: LBPA ENS CACHAN/CNRS/UMR 8113 61, avenue du Président Wilson, 94235 CACHAN CEDEX (France) ACKNOWLEDGEMENT This thesis would not have been done possibly without the support of many people.
    [Show full text]
  • Structures of Partition Protein Para with Nonspecific DNA and Parb Effector Reveal Molecular Insights Into Principles Governing Walker-Box DNA Segregation
    Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation Hengshan Zhang and Maria A. Schumacher Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA Walker-box partition systems are ubiquitous in nature and mediate the segregation of bacterial and archaeal DNA. Well-studied plasmid Walker-box partition modules require ParA, centromere–DNA, and a centromere-binding protein, ParB. In these systems, ParA–ATP binds nucleoid DNA and uses it as a substratum to deliver ParB-attached cargo DNA, and ParB drives ParA dynamics, allowing ParA progression along the nucleoid. How ParA–ATP binds nonspecific DNA and is regulated by ParB is unclear. Also under debate is whether ParA polymerizes on DNA to mediate segregation. Here we describe structures of key ParA segregation complexes. The ParA–β,γ-imidoadenosine 5′-triphosphate (AMPPNP)–DNA structure revealed no polymers. Instead, ParA–AMPPNP dimerization creates a multifaceted DNA-binding surface, allowing it to preferentially bind high-density DNA regions (HDRs). DNA- bound ParA–AMPPNP adopts a dimer conformation distinct from the ATP sandwich dimer, optimized for DNA association. Our ParA–AMPPNP–ParB structure reveals that ParB binds at the ParA dimer interface, stabilizing the ATPase-competent ATP sandwich dimer, ultimately driving ParA DNA dissociation. Thus, the data indicate how harnessing a conformationally adaptive dimer can drive large-scale cargo movement without the requirement for polymers and suggest a segregation mechanism by which ParA–ATP dimers equilibrate to HDRs shown to be lo- calized near cell poles of dividing chromosomes, thus mediating equipartition of attached ParB–DNA substrates.
    [Show full text]
  • The Replication Factor C Clamp Loader Requires Arginine Finger Sensors to Drive DNA Binding and Proliferating Cell Nuclear Antig
    THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 281, NO. 46, pp. 35531–35543, November 17, 2006 Printed in the U.S.A. The Replication Factor C Clamp Loader Requires Arginine Finger Sensors to Drive DNA Binding and Proliferating Cell Nuclear Antigen Loading*ࡗ Received for publication, June 26, 2006, and in revised form, September 14, 2006 Published, JBC Papers in Press, September 15, 2006, DOI 10.1074/jbc.M606090200 Aaron Johnson‡, Nina Y. Yao‡, Gregory D. Bowman§, John Kuriyan¶ʈ, and Mike O’Donnell‡** From the **Laboratory of DNA Replication, Howard Hughes Medical Institute and ‡Rockefeller University, New York, New York 10021, the ¶Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, California 94720, the ʈPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and the §Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 ,Replication factor C (RFC) is an AAA؉ heteropentamer that The DNA polymerase binds to the processivity clamp protein couples the energy of ATP binding and hydrolysis to the loading which completely encircles DNA. The clamp slides on DNA Downloaded from of the DNA polymerase processivity clamp, proliferating cell and is pulled along by the polymerase during chain extension, nuclear antigen (PCNA), onto DNA. RFC consists of five sub- continuously holding polymerase to DNA and constraining it units in a spiral arrangement (RFC-A, -B, -C, -D, and -E, corre- to act in a highly processive manner. sponding to subunits RFC1, RFC4, RFC3, RFC2, and RFC5, The eukaryotic ring-shaped processivity factor, proliferating -respectively). The RFC subunits are AAA؉ family proteins and cell nuclear antigen (PCNA),2 is a trimer of three identical sub http://www.jbc.org/ the complex contains four ATP sites (sites A, B, C, and D) units arranged head-to-tail to generate a ring with a large cen- located at subunit interfaces.
    [Show full text]