6BQ2

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases.

Sekula, B.Dauter, Z.

(2018) Biochem. J. 475: 787-802

  • DOI: 10.1042/BCJ20170900
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyamines are linear polycationic compounds that play a crucial role in the growth and development of higher plants. One triamine (spermidine, SPD) and two tetraamine isomers (spermine, SPM, and thermospermine, TSPM) are obtained by the transfer of ...

    Polyamines are linear polycationic compounds that play a crucial role in the growth and development of higher plants. One triamine (spermidine, SPD) and two tetraamine isomers (spermine, SPM, and thermospermine, TSPM) are obtained by the transfer of the aminopropyl group from decarboxylated S -adenosylmethionine to putrescine and SPD. These reactions are catalyzed by the specialized aminopropyltransferases. In that respect, plants are unique eukaryotes that have independently evolved two enzymes, thermospermine synthase (TSPS), encoded by the gene ACAULIS5 , and spermine synthase, which produce TSPM and SPM, respectively. In this work, we structurally characterize the ACAULIS5 gene product, TSPS, from the model legume plant Medicago truncatula ( Mt ). Six crystal structures of Mt TSPS - one without ligands and five in complexes with either reaction substrate (SPD), reaction product (TSPM), or one of three cofactor analogs (5'-methylthioadenosine, S -adenosylthiopropylamine, and adenosine) - give detailed insights into the biosynthesis of TSPM. Combined with small-angle X-ray scattering data, the crystal structures show that Mt TSPS is a symmetric homotetramer with an interdomain eight-stranded β-barrel. Such an assembly and the presence of a hinge-like feature between N-terminal and C-terminal domains give the protein additional flexibility which potentially improves loading substrates and discarding products after the catalytic event. We also discuss the sequence and structural features around the active site of the plant aminopropyltransferases that distinguish them from each other and determine their characteristic substrate discrimination.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.,From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and scg34@cam.ac.uk.,Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China.,Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy. luigi.messori@unifi.it.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt. Electronic address: ahmed.belal@alexu.edu.eg.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Sanofi-Aventis Pharma Deutschland GmbH, Frankfurt am Main, Germany.,College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC, Australia.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A. bartosz.sekula@nih.gov.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. ruffo@unina.it.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China.,Charles River , Chesterford Research Park , Saffron Walden CB10 1XL , U.K.,Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea. Sunglee@chosun.ac.kr.,Department of Immunology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.,The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Department of Analytical & Pharmaceutical Chemistry, Faculty of Pharmacy & Drug Manufacturing, Pharos University in Alexandria, Egypt.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States. wli@uthsc.edu.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Pharmacology and Toxicology, Faculty of Medicine and Medical Centre, American University of Beirut, Beirut, Lebanon; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt. Electronic address: ae88@aub.edu.lb.,Pathology and Laboratory Medicine Service, VA Medical Center at Birmingham, Birmingham, AL, 35294, United States.,From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; BioSupraMol Core Facility, Freie Universität Berlin, 14195 Berlin, Germany.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. ilia.voskoboinik@petermac.org.,Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, IBIS et PROTEO, Université Laval, Pavillon Charles-Eugène Marchand, Québec, Canada.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Biotechnology Research Centre, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Institute of Molecular Biology and Biophysics, ETH Zurich, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.,Department of Pharmacy, University of Pisa, 56126 Pisa, Italy. tiziano.marzo@unipi.it.,Ion Mobility-Mass Spectrometry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia.,Department of Dermatology, Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, 35294, United States.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.,National Center for Protein Science Shanghai , Shanghai, China.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. giarita.ferraro@gmail.com.,X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India.,CHDI Management/CHDI Foundation , 6080 Center Drive , Los Angeles , California 90045 , United States.,Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland.,Department of Pharmacology and Toxicology, Faculty of Medicine and Medical Centre, American University of Beirut, Beirut, Lebanon.,Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea.,Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.,Axe Molecular Endocrinology and Nephrology, CHU de Québec Research Center, Department of Molecular Medicine, Laval University, Québec, Canada.,Department of Veterans Affairs Medical Center, Memphis, TN, 38104, United States.,Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Molecular Biology Institute, University of California, Los Angeles, CA, USA.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India ashish_arora@cdri.res.in.,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, United States.,GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany. Electronic address: chfreund@zedat.fu-berlin.de.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. antonello.merlino@unina.it.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. cuccioli@unina.it.,Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.,College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.,Department of Photon Science, Stanford University, Stanford, United States.,Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. ilia.voskoboinik@petermac.org.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China.,Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Egypt.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. amelia.brennan@petermac.org.,Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, UK.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France. rochel@igbmc.fr.,Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China. Electronic address: cong@sibcb.ac.cn.,Microbiology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.,GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA. Electronic address: david.n.deaton@gsk.com.,Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA.,GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA.,Institute for Photonics and Advanced Sensing, The School of Biological Sciences, The University of Adelaide, North Tce, Adelaide, South Australia, 5005, Australia.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel; dan.tawfik@weizmann.ac.il Bar-Even@mpimp-golm.mpg.de.,Physical and Theoretical Chemistry Laboratory, University of Oxford, OX1 3QZ Oxford, United Kingdom.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; john.rubinstein@utoronto.ca.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology TMP, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany.,the Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, United Kingdom.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. Electronic address: fengyg@qibebt.ac.cn.,Department of Material Science, Graduate School of Science, Osaka City University Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan.,Ion Mobility-Mass Spectrometry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,Charles River , Leiden 2333 CR , Netherlands.,GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; dan.tawfik@weizmann.ac.il Bar-Even@mpimp-golm.mpg.de.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology TMP, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany; Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany.,Institute of Microbial Technology, Chandigarh, Council of Scientific and Industrial Research, Chandigarh 160 036, India.,Department of Structural Biology, Stanford University, Stanford, United States.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermospermine synthase ACAULIS protein
A, B
331Medicago truncatulaMutation(s): 0 
Gene Names: 11439099
EC: 2.5.1.16
Find proteins for G7K2D1 (Medicago truncatula)
Go to UniProtKB:  G7K2D1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.530α = 90.00
b = 80.530β = 90.00
c = 164.360γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-27 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Sekula, B., Dauter, Z.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesThe Intramural Research Program

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references