5U0I

C-terminal ankyrin repeats from human kidney-type glutaminase (KGA) - tetragonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.423 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats.

Pasquali, C.C.Islam, Z.Adamoski, D.Ferreira, I.M.Righeto, R.D.Bettini, J.Portugal, R.V.Yue, W.W.Gonzalez, A.Dias, S.M.G.Ambrosio, A.L.B.

(2017) J. Biol. Chem. 292: 11572-11585

  • DOI: 10.1074/jbc.M117.787291
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. ...

    On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. However, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform, glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. To obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France.,Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, sandra.dias@lnbio.cnpem.br.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan. chinyuchen@cc.ncu.edu.tw.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and William.Royer@umassmed.edu.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Infinitus (China) Co. Ltd. , Guangzhou 510663 , P. R. China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: jtzheng@sjtu.edu.cn.,Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and.,the Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom.,Department of Biochemistry, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, Vandoeuvre-les-Nancy Cedex, France.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands.,School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK. jyl@mrc-lmb.cam.ac.,From the Departments of Structural Biology and.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Institute of Biochemistry, Graz University of Technology, Graz, Austria.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA.,School of Biochemistry, Devi Ahilya University, Indore, India.,Department of Biochemistry, University of Oxford, Oxford, UK.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, andre.ambrosio@lnbio.cnpem.br.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. emarcos82@gmail.com.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Cyrus Biotechnology, Seattle, WA, USA.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , P. R. China.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom; walker@mrc-mbu.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Department of Microbiology, Immunology & Molecular Genetics, University of California at Los Angeles, Los Angeles, California.,Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California, Irvine , Irvine , California 92697-3900 , United States.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,the School of Electrical and Computer Engineering, University of Campinas, São Paulo 13083-852, Brazil, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105 charles.rock@stjude.org.,School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , P. R. China.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.,Department of Microbiology and Immunology, University of Otago, 9016 Dunedin, New Zealand.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaminase kidney isoform, mitochondrial
A, B
140Homo sapiensMutation(s): 0 
Gene Names: GLS (GLS1, KIAA0838)
EC: 3.5.1.2
Find proteins for O94925 (Homo sapiens)
Go to Gene View: GLS
Go to UniProtKB:  O94925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.423 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.144 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.290α = 90.00
b = 75.290β = 90.00
c = 88.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXCDphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil2014/20673-2

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references, Structure summary
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references, Derived calculations
  • Version 1.3: 2019-04-17
    Type: Author supporting evidence, Data collection