5TQN

Lipoxygenase-1 (soybean) L546A mutant at 293K

  • Classification: OXIDOREDUCTASE
  • Organism(s): Glycine max
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2016-10-24 Released: 2017-11-01 
  • Deposition Author(s): Poss, E.M., Fraser, J.S., Gee, C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Center for Research Resources 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Hu, S.Offenbacher, A.R.Thompson, E.M.Gee, C.L.Wilcoxen, J.Carr, C.A.M.Prigozhin, D.M.Yang, V.Alber, T.Britt, R.D.Fraser, J.S.Klinman, J.P.

(2019) J.Am.Chem.Soc. 141: 1555-1567

  • DOI: 10.1021/jacs.8b10992
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-indep ...

    Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen-deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein-solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.


    Organizational Affiliation

    Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK.,Center for Drug Discovery, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address: ervin.fodor@path.ox.ac.uk.,Synchrotron Radiation Research Section of MCL, National Cancer Institute, S Cass Ave 9700, Argonne, IL, U.S.A. milosz.ruszkowski@nih.gov.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and alan.cartmell2@newcastle.ac.uk.,Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy.,JEM Utilization Center, Human Spaceflight Technology Directorate , Japan Aerospace Exploration Agency (JAXA) , 2-1-1 Sengen , Tsukuba-shi , Ibaraki 305-8505 , Japan.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA.,Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain. Electronic address: adoracion.gomez@uam.es.,Center for Structural Biology, and.,Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland ausra.domanska@helsinki.fi sarah.butcher@helsinki.fi.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,Living Systems Institute, University of Exeter, Exeter, UK.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A. adha@ufl.edu.,School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden; adnane.achour@ki.se T.van_Hall@lumc.nl.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. nyasui@okayama-u.ac.jp.,State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000, China.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064 harry@nuvolari.ucsc.edu.,Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,New York Structural Biology Center, New York, NY, USA.,Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: liuzhj@shanghaitech.edu.cn.,Max Planck Institute for Developmental Biology, Tübingen, Germany.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: mko2@cdc.gov.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.,a Molecular Cancer Research Group, Department of Medical Biology , University of Tromsø -The Arctic University of Norway , Tromsø , Norway.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045.,Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and jcordero@uthsc.edu.,Howard Hughes Medical Institute, Chevy Chase, United States.,MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen 361102, P.R. China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; adnane.achour@ki.se T.van_Hall@lumc.nl.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China. Electronic address: wmxing@sibs.ac.cn.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: kasper.rand@sund.ku.dk.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark.,Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720; view@berkeley.edu monica.balsera@csic.es.,Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China.,Department of Biological Chemistry and Pharmacology , The Ohio State University , Columbus , Ohio 43210 , United States.,d Peptide Chemistry Science Technology Platform , The Francis Crick Institute , London , UK.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Department of Chemistry, University of Florida, Gainesville, FL, U.S.A.,Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.,Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Physics, Ohio State University, Columbus, OH 43210.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China. Electronic address: wangyc@njau.edu.cn.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2880, Denmark.,Department of Molecular Physiology and Biophysics.,Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, 2000 Neuchâtel, Switzerland.,Department of Biology, Technische Universität Darmstadt, D64287 Darmstadt, Germany.,Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.,Department of Biochemistry and Molecular Biology and ‡Department of Immunology, Mayo Clinic , Rochester, Minnesota 55905, United States.,Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Daejeon, South Korea.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Pharmaceutical Chemistry and Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, KS, USA.,Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. Electronic address: luigi.messori@unifi.it.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: leila@chem.ku.dk.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China.,Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Graduate School of Medical Science and Engineering, College of Life Science and Bioengineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,c Molecular Cell Biology of Autophagy Laboratory , The Francis Crick Institute , London , UK.,School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA. Electronic address: aihar001@umn.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, 37007 Salamanca, Spain.,Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milan, 20133 Milan, Italy.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States.,Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China.,Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, 37008 Salamanca, Spain view@berkeley.edu monica.balsera@csic.es.,Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.,b Structural Biology , The Francis Crick Institute , London , UK.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK.,Novartis Institutes for Biomedical Research (China), Zhangjiang Hi-Tech Park , Pudong New Area, Shanghai 201203, China.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK. Electronic address: jonathan@strubi.ox.ac.uk.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: erica@scripps.edu.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. Electronic address: gcdu@jiangnan.edu.cn.,Centro Universitario de la Defensa, Ctra. Huesca s/n, 50090 Zaragoza, Spain.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Department of Pathology, The University of Chicago, Chicago, IL, United States.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi, 13, 56124 Pisa, Italy; Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Cell Therapy Institute, Nova Southeastern University, Fort Lauderdale, FL 33314; and.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA.,Department of Bioengineering and Therapeutic Science , University of California, San Francisco , San Francisco , California 94158 , United States.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045; tatiana.kutateladze@ucdenver.edu.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Molecular Physiology and Biophysics, terunaga.nakagawa@vanderbilt.edu.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,Campus Chemical Instrument Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Committee on Microbiology, The University of Chicago, Chicago, IL, United States.,College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,University of Chinese Academy of Sciences, Beijing, China.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and.,Department of Food and Nutrition, Duksung Women's University, Seoul, South Korea.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Umeå Center for Microbial Research, Umeå University, Umeå, Sweden.,Department of Chemistry , University of California, Davis , Davis , California 95695 , United States.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,DiscoveRx Corporation , Fremont, California 94538, United States.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain. Electronic address: pereda@usal.es.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre , 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093-0378, USA.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. a_yama@cc.okayama-u.ac.jp.,Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed linoleate 13S-lipoxygenase-1
A, B
839Glycine maxMutation(s): 1 
Gene Names: LOX1.1 (LOX1)
EC: 1.13.11.12
Find proteins for P08170 (Glycine max)
Go to UniProtKB:  P08170
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.519α = 90.00
b = 92.656β = 93.47
c = 100.751γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM113432
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR022393-01
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM025765

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection
  • Version 1.2: 2019-05-15
    Type: Data collection, Database references