6FRW

X-ray structure of the levansucrase from Erwinia tasmaniensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora.

Polsinelli, I.Caliandro, R.Salomone-Stagni, M.Demitri, N.Rejzek, M.Field, R.A.Benini, S.

(2019) Int. J. Biol. Macromol. 127: 496-501

  • DOI: 10.1016/j.ijbiomac.2019.01.074

  • PubMed Abstract: 
  • Erwinia tasmaniensis is an epiphytic bacterium related to the plant pathogen Erwinia amylovora, the etiological agent of fire blight. In this study the levansucrase from E. tasmaniensis (EtLsc) has been compared with the homologous enzyme from E. amy ...

    Erwinia tasmaniensis is an epiphytic bacterium related to the plant pathogen Erwinia amylovora, the etiological agent of fire blight. In this study the levansucrase from E. tasmaniensis (EtLsc) has been compared with the homologous enzyme from E. amylovora (EaLsc). We characterized the enzymatic activity and compared the products profile of both enzymes by High Performance Anion Exchange Chromatography coupled with Pulsed Amperometric Detector (HPAEC-PAD). Moreover we determined the crystal structure of EtLsc to understand the structural peculiarity causing the different product profiles of the two homologues. EtLsc exhibits increased efficiency in the production of FOS, resulting in a better catalyst for biotechnological synthesis than EaLsc. Based on our results, we propose that the role of this enzyme in the life cycle of the two bacteria is most likely related to survival, rather than linked to pathogenicity in E. amylovora.


    Organizational Affiliation

    Department of Medicine , University of Wisconsin-Madison , 3341 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio. rosa.lapalombella@osumc.edu john.byrd@osumc.edu.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA. Michael.Acker@novartis.com.,The RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sato-gun, Hyogo, 678-5248, Japan.,the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.,School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,iHuman Institute, ShanghaiTech University, Shanghai, China.,Department of Hematology, Hôpital Necker, Assistance Publique Hôpitaux de Paris, University Paris Descartes, 75006 Paris, France.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India sgourinath@mail.jnu.ac.in.,William S. Middleton Memorial Veterans Hospital , 2500 Overlook Terr. , Madison , Wisconsin 53705 , United States.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.,Departments of Biochemistry and Biophysics and Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Medical Microbiology and Immunology , University of Wisconsin-Madison , 4203 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Bioorganic Chemistry and Bio-Crystallography laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy. Electronic address: stefano.benini@unibz.it.,Division of Cell Signaling and Immunology and University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,Xtal BioStructures Inc., Natick, MA 01760, USA.,Department of Pharmacology, Monash University, Clayton, VIC 3800, Australia.,CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. sunlf17@ustc.edu.cn.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia. Electronic address: M.Maher@latrobe.edu.au.,Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Clinical Medicine, Aarhus University, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark.,Small Molecule Screening Facility, Carbone Cancer Center , University of Wisconsin-Madison , 1111Highland Ave. , Madison , Wisconsin 53705 , United States.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. mirko.zaffagnini3@unibo.it.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Paris Saclay, 91190 Paris, France.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. michelet@ibpc.fr.,Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084 China.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.,College of Veterinary Medicine, The Ohio State University, Columbus, Ohio.,HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK g.l.challis@warwick.ac.uk.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. lemaire@ibpc.fr.,From the Department of Biochemistry and Molecular Biology, ncjs@mail.ubc.ca.,Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. crozet@ibpc.fr.,Center for Biostatistics, The Ohio State University, Columbus, Ohio.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio.,3Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China.,5Present Address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,iHuman Institute, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, USA.,the Centre for Blood Research, and.,Department of Pathology, St. Olavs Hospital, Trondheim, Norway.,School of Medicine and Dentistry , University of Rochester Medical Center , 601 Elmwood Ave. , Rochester , New York 14620 , United States.,Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, Trieste 34149, Italy.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.,Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia.,Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland.,LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse 6, Marburg 35032, Germany.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia.,LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. Electronic address: jsunkim@chonnam.ac.kr.,Bio-Pharmaceutical Analysis Section (Bio-PhASe), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy. daniele.tedesco@unibo.it.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Plexxikon Inc., Berkeley, California.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Sorbonne Paris Cité, Paris, France.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, DK-8000, Aarhus C, Denmark.,Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.,INSERM U944, Institute of Hematology, St. Louis Hospital, 75010 Paris, France.,Department of Picobiology/Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.,Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226 CNRS Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France. julien.henri@sorbonne-universite.fr.,Queensland Brain Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands. b.j.c.janssen@uu.nl.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus C, Denmark. pn@mbg.au.dk.,MRC, Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, U.K.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Germany.,Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.,Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,4Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX), Germany.,Department of Dermatology, Aarhus University Hospital, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark.,Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Membrane Biology, Beijing, 100084 China.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, USA.,From the Department of Biochemistry and Molecular Biology.,Department of Chemistry "Giacomo Ciamician", University of Bologna, via Selmi 2, 40126 Bologna, Italy. simona.fermani@unibo.it.,Department of Clinical Medicine, Aarhus University, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark. lars.iversen@clin.au.dk.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,the Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; l.rash@uq.edu.au glenn.king@imb.uq.edu.au.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR47UH, United Kingdom.,Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA.,Medical Research Council Protein Phosphorylation Unit, School of Life Sciences, Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.,Cayman Chemical Co., Ann Arbor, MI 48108, USA.,Bioorganic Chemistry and Bio-Crystallography laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Dermatology, Aarhus University Hospital, P.P. Oerumsgade 11, DK-8000, Aarhus C, Denmark. lars.iversen@clin.au.dk.,Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.,Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , SGC Center for Chemical Biology, 120 Mason Farm Rd. , Chapel Hill , North Carolina 27599 , United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Levansucrase (Beta-D-fructofuranosyl transferase)
A
411Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99)Mutation(s): 0 
Gene Names: lsc
EC: 2.4.1.10
Find proteins for B2VCC3 (Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99))
Go to UniProtKB:  B2VCC3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.493α = 90.00
b = 128.493β = 90.00
c = 58.945γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Free University of BolzanoItaly1440

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release