5EL1

Crystal structure of deoxyribose-phosphate aldolase from Escherichia coli (K58E-Y96W mutant) after acetaldehyde treatment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies.

Dick, M.Hartmann, R.Weiergraber, O.H.Bisterfeld, C.Classen, T.Schwarten, M.Neudecker, P.Willbold, D.Pietruszka, J.

(2016) Chem Sci 7: 4492-4502

  • DOI: 10.1039/c5sc04574f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance ...

    2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance towards high concentrations of acetaldehyde, its natural substrate. While numerous studies have been performed searching for new, more acetaldehyde-resistant DERAs, the mechanism underlying this deactivation process has remained elusive. By using NMR spectroscopy on both the protein and the small-molecule scale, we could show that a reaction product binds to the inner part of the enzyme, and that this effect can be partly reversed via heating. The crystal structure of DERA before and after acetaldehyde incubation was determined at high resolution, revealing a covalently bound reaction product bridging the catalytically active lysine (K167) to a nearby cysteine (C47) in the deactivated enzyme. A reaction mechanism is proposed where crotonaldehyde as the aldol product of two acetaldehyde molecules after water elimination forms a Schiff base with the lysine side chain, followed by Michael addition of the cysteine thiol group to the C β atom of the inhibitor. In support of this mechanism, direct incubation of DERA with crotonaldehyde results in a more than 100-fold stronger inhibition, compared to acetaldehyde, whereas mutation of C47 gives rise to a fully acetaldehyde-resistant DERA. Thus this variant appears perfectly suited for synthetic applications. A similar diagnostic and preventive strategy should be applicable to other biocatalysts suffering from mechanism-based inhibition by a reactive substrate, a condition that may be more common than currently appreciated in biotechnology.


    Organizational Affiliation

    Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA. frastinejad@sbpdiscovery.org.,MARUWA Foods and Biosciences, Inc. 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan.,Department of Pharmacology, Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. jbriggs@mrc-lmb.cam.ac.uk.,Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation.,KU-KIST Graduate School of Converging Science and Technology , Korea University , Seoul 136-701 , Korea.,Tumor Microenvironment and Resistance to Treatment Lab, Institut de Recherche en Cancrologie de Montpellier, 34090 Montpellier, France; Institut du Cancer Montpellier, 34090 Montpellier, France; Universit Montpellier, 34298 Montpellier, France.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.,Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084.,Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India. Electronic address: sekar@iisc.ac.in.,Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia. b.collins@imb.uq.edu.au.,Dept. Pharmacokinetics, Toxicology and Targeting, Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA, 92023, USA.,Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.,Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: mckenna@ufl.edu.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Faculty of Biotechnology, University of Wrocław, Wrocław, Poland teresa.olczak@uwr.edu.pl.,Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland. michael.hothorn@unige.ch.,Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.,Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Campus E8.1, 66123, Saarbrücken, Germany.,Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Department of Physics, Indian Institute of Science, Bangalore 560012, India.,Roger Adams Laboratory, Department of Biochemistry, University of llinois at Urbana-Champaign, Urbana, United States.,Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China.,Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK. djo30@cam.ac.uk.,CICbioGUNE, Derio, Spain.,Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA. xuehua.zhong@wisc.edu.,Malaysia Genome Institute, National Institute of Biotechnology Malaysia, Jalan Bangi, 43000 Kajang, Selangor, Malaysia.,Present address: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.,School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.,Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California-San Diego, La Jolla, CA, 92093, USA.,Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States.,Pennsylvania State University, UNITED STATES.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.,Pennsylvania State University, Chemistry, UNITED STATES.,State Key Laboratory of Molecular Biology, Shanghai Science Research Center, Chinese Academy of Sciences 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, China; rgzhang@sibcb.ac.cn jinwei.zhu@sibcb.ac.cn.,From the Interdepartmental Graduate Program in Translational Biology and Molecular Medicine.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030 and timothyp@bcm.edu.,Pennsylvania State University, Chemistry, 220 Chemistry Building, Penn State University, 16802, University Park, UNITED STATES.,LumiSTAR Biotechnology Incorporation, Nangang District, Taipei City, 115, Taiwan.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, Goethe University of Frankfurt, 60590 Frankfurt, Germany.,Department of Chemistry and Industrial Chemistry, University of Pisa, I-56126 Pisa, Italy.,Institute of Biostatistics, Leibniz University, Hannover, Germany.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, and.,Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: hymowitz@gene.com.,Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA.,Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, USA. Feradical@utsa.edu.,Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.,Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA harry@nuvolari.ucsc.edu.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China.,Novartis Institutes for Biomedical Research, 5300 Chiron Way , Emeryville , California 94608 , United States.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA. Electronic address: roger.b.sutton@ttuhsc.edu.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Vossius & Partner, Munich, Germany.,Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada. rc4@ualberta.ca.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA. xuehua.zhong@wisc.edu.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China 100084.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China. Electronic address: wuzhl@cib.ac.cn.,RIKEN Structural Biology Laboratory 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Max von Pettenkofer-Institute, Department of Virology, Ludwig Maximilians University, 80336 Munich, Germany.,Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.,Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany . Email: j.pietruszka@fz-juelich.de.,Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany. Electronic address: wibke.diederich@staff.uni-marburg.de.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee , Dow Street , Dundee DD1 5EH , Scotland , United Kingdom.,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,Project Group Translational Medicine and Pharmacology, Frauenhofer Institute for Molecular Biology and Applied Ecology, 60590 Frankfurt, Germany.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China. Electronic address: wangg@cib.ac.cn.,Institute of Medical Virology, Justus Liebig University, Giessen, Germany.,Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Laboratory of Protein Engineering , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland.,Graduate School of Biomedical Engineering Tohoku University 2-1 Seiryomachi, Aoba Sendai 980-8575 Japan.,Department of Pharmacology, University of California, Davis, CA, USA.,Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.,Astellas Pharma., Tsukuba, Japan.,Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53705, USA; Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil. Electronic address: marcos.fontes@unesp.br.,Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina , Universitat Autònoma de Barcelona , E-08193 Barcelona , Spain.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology Research Center, Malaysia.,Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, Korea.,Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd Mail Stop #3030, Kansas City, KS 66160, USA.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany; The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia. Electronic address: Max.Cryle@monash.edu.,Department of Chemistry, University of California, Davis, CA, USA.,Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore. Electronic address: dbsmokh@nus.edu.sg.,Zentrum für Arzneimittelforschung, -entwicklung, und -sicherheit, Goethe University of Frankfurt, 60590 Frankfurt, Germany.,Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, USA.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.,Department Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Campus E8.1, 66123, Saarbrücken, Germany.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan; Daiichi University of Pharmacy, 22-1 Tamagawa, Minami, Fukuoka 815-8511, Japan.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.,Department of Chemistry, University of Florence, I-50019 Sesto Fiorentino (FI), Italy.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030 and.,Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama, 230-0045, Japan.,Department of Chemistry, University of Texas, Edinburgh, TX, USA.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. longs@mskcc.org.,Research School of Chemistry, Australian National University, Canberra, ACT, Australia.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Aurigene Discovery Technologies, Ltd., Bengaluru and Hyderabad, India.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Hyogo, Japan.,RIKEN Center for Biosystems Dynamics Research 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan.,Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA.,Institute of Integrative Biology, University of Liverpool, Liverpool, U.K.,Division of Structural and Synthetic Biology RIKEN Center for Life Science Technologies 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan.,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892.,Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama, 230-0045, Japan. Electronic address: jtame@yokohama-cu.ac.jp.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology Research Center, Malaysia.,Institute of Medical Virology, Justus Liebig University, Giessen, Germany. Electronic address: john.ziebuhr@viro.med.uni-giessen.de.,State Key Laboratory of Molecular Biology, Shanghai Science Research Center, Chinese Academy of Sciences 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, China.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.,Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA. Electronic address: shenb@scripps.edu.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.,Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgeri 1, 34127 Trieste, Italy. Electronic address: sgeremia@units.it.,Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland.,Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.,School of Dentistry, Institute of Clinical Sciences, University of Liverpool, Liverpool, U.K.,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, China. jmdu@sibs.ac.cn.,The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 Jiangsu, China.,Department of Chemistry, Yale University, New Haven, CT 06520.,Department of Pathology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA.,Institute of Biophysics, Ulm University, Ulm, Germany.,School of Biological Sciences, University of Essex, Colchester, U.K.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany.,NDBio Therapeutics, Inc., 32 Songdogwahak-ro , Yeonsu-gu , Incheon 21984 , Republic of Korea.,Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect, Shandong Agricultural University, Tai'an, China; College of Life Sciences, Shandong Agricultural University, Tai'an, China. Electronic address: zhuchunyuan@sdau.edu.cn.,Department of Molecular Genetics Osaka University 3-1 Yamadaoka, Suita Osaka 565-0871 Japan.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Korea.,Bioproduction Research Institute, Japan.,Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.,Chemical Kinomics Research Center , Korea Institute of Science and Technology (KIST) , Seoul 02792 , Korea.,Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine , University of Oxford , Oxford , United Kingdom.,Chair of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, 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, China.,ChromoTek GmbH, Planegg, Germany.,Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA.,Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany.,Department of Cancer Biology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States.,Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.,Biological Science Imaging Resource, Department of Biological Sciences, The Florida State University, 89 Chieftan Way, Rm 119, Tallahassee, FL 32306, USA.,School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.,Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA.,Structural Genomics Consortium, 101 College Street, Toronto, Ontario, Canada.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology Research Center, Malaysia.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore. Electronic address: chandra@bii.a-star.edu.sg.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China.,Université de Lorraine, INRA, IAM, Nancy, France.,University of Chinese Academy of Sciences, Beijing, China.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Physiology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.,Department of Chemistry, University of California, Davis, CA, USA jbames@ucdavis.edu jwhell@ucdavis.edu.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology Research Center, Malaysia. Electronic address: adamleow@upm.edu.my.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan. Electronic address: aktanaka@riken.jp.,Present address: Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 4195, USA.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084. Electronic address: hongweiwang@tsinghua.edu.cn.,Department of Medicine , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,College of Plant Protection, Shandong Agricultural University, Tai'an, China; Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect, Shandong Agricultural University, Tai'an, China.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgeri 1, 34127 Trieste, Italy.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Lille University, UMR8576, CNRS, 59000, Lille, France.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. jbriggs@mrc-lmb.cam.ac.uk.,Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.,Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. dlyumkis@salk.edu.,Department of Bioinformatics, Alagappa University, Karaikudi 630003, India.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.,Electron Microscope Unit, The University of New South Wales, Kensington, New South Wales, Australia.,Molecular Biology and Biochemistry, University of California Irvine, McGaugh Hall, Irvine, CA 92697-3900, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21205, USA.,Verna Marrs McLean Department of Biochemistry and Molecular Biology, and.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China.,the Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Division of Molecular Biological-Biochemical Processing Technology, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.,Department of Biochemistry, Weill Cornell Medical College, New York, United States.,Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road, La Jolla, California 92037, United States.,School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; yong.xiong@yale.edu.,Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA.,Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA. mckenna@ufl.edu.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China; and.,Morgridge Institute for Research, Madison, WI, USA.,Institute of Medical Virology, University Hospital Frankfurt, 60596 Frankfurt, Germany.,Biomedical Research Institute, Japan.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Pharmacology, University of California, Davis, CA, USA jbames@ucdavis.edu jwhell@ucdavis.edu.,Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.,Research School of Chemistry, Australian National University, Canberra, ACT, Australia. colin.jackson@anu.edu.au.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.,Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,OmicScouts GmbH, Freising, Germany.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.,Lille University, UMR8576, CNRS, 59000, Lille, France. isabelle.landrieu@univ-lille1.fr.,Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyribose-phosphate aldolase
A
265Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: deoC (dra, thyR)
EC: 4.1.2.4
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
1BO
Query on 1BO

Download SDF File 
Download CCD File 
A
1-BUTANOL
BUTAN-1-OL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.117 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.830α = 90.00
b = 53.300β = 98.29
c = 37.810γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references