6ET9

Structure of the acetoacetyl-CoA-thiolase/HMG-CoA-synthase complex from Methanothermococcus thermolithotrophicus at 2.75 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site.

Vogeli, B.Engilberge, S.Girard, E.Riobe, F.Maury, O.Erb, T.J.Shima, S.Wagner, T.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 3380-3385

  • DOI: 10.1073/pnas.1718649115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many reactions within a cell are thermodynamically unfavorable. To efficiently run some of those endergonic reactions, nature evolved intermediate-channeling enzyme complexes, in which the products of the first endergonic reactions are immediately co ...

    Many reactions within a cell are thermodynamically unfavorable. To efficiently run some of those endergonic reactions, nature evolved intermediate-channeling enzyme complexes, in which the products of the first endergonic reactions are immediately consumed by the second exergonic reactions. Based on this concept, we studied how archaea overcome the unfavorable first reaction of isoprenoid biosynthesis-the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA catalyzed by acetoacetyl-CoA thiolases (thiolases). We natively isolated an enzyme complex comprising the thiolase and 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGCS) from a fast-growing methanogenic archaeon, Methanothermococcus thermolithotrophicus HMGCS catalyzes the second reaction in the mevalonate pathway-the exergonic condensation of acetoacetyl-CoA and acetyl-CoA to HMG-CoA. The 380-kDa crystal structure revealed that both enzymes are held together by a third protein (DUF35) with so-far-unknown function. The active-site clefts of thiolase and HMGCS form a fused CoA-binding site, which allows for efficient coupling of the endergonic thiolase reaction with the exergonic HMGCS reaction. The tripartite complex is found in almost all archaeal genomes and in some bacterial ones. In addition, the DUF35 proteins are also important for polyhydroxyalkanoate (PHA) biosynthesis, most probably by functioning as a scaffold protein that connects thiolase with 3-ketoacyl-CoA reductase. This natural and highly conserved enzyme complex offers great potential to improve isoprenoid and PHA biosynthesis in biotechnologically relevant organisms.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA adam.renslo@ucsf.edu ychen1@health.usf.edu.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095.,Department of Genome Sciences, University of Washington, Seattle, United States.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Molecular Biosciences, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.,Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. stefano.ciurli@unibo.it.,Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030; rclubb@mbi.ucla.edu ton-that.hung@uth.tmc.edu.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina, 27710, USA. awilliam@pasteur.fr.,Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.,Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway. kaarebj@kjemi.uio.no.,Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wfeng@ibp.ac.cn.,Department of Mathematics, University of York, York YO10 5DD, United Kingdom.,Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guizhou Medical University, Guiyang, China.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. yingxuxu@shsmu.edu.cn.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: ckerfeld@lbl.gov.,JSC Spronk, Vilnius, Lithuania.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA. zaw@uga.edu.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. jysuh@snu.ac.kr.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada. burrowl@mcmaster.ca.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA.,School of Life Sciences and Technology, Tongji University, Shanghai, China.,Broad Institute of MIT and Harvard, Cambridge, MA, United States of America.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom.,Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.,Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.,MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa. Electronic address: valerie.mizrahi@uct.ac.za.,Department of Biochemistry, University of Washington, Seattle, United States.,Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.,Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, NO-0372 Oslo, Norway. g.a.loset@ibv.uio.no.,Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui 230027, China.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America.,School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK.,State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, 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, 333 Haike Road, Shanghai 201210, China.,Howard Hughes Medical Institute, Departments of Physiology and Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.,CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia.,Drug Discovery Group Cancer Research UK Manchester Institute, Manchester, UK.,the Departments of Life Sciences and.,Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil. kleber.franchini@lnbio.cnpem.br.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,D. E. Shaw Research, New York, NY, USA.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.,The Hamburg Centre for Ultrafast Imaging, Germany.,Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.,Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain. xjuan@iqfr.csic.es.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,Department of Microbiology, University of Washington, Seattle, United States.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada. howell@sickkids.ca.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. juliana.oliveira@lnbio.cnpem.br.,Chemistry and Biochemistry, University of Arizona, 1041 East Lowell Drive, Biosciences West, Tucson, AZ 85281, USA.,European XFEL GmbH, Schenefeld, Germany.,Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany tristan.wagner@mpi-marburg.mpg.de.,Department of Chemistry, University of California, Berkeley, California.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. chengq@shsmu.edu.cn.,Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Institut de Biologie Structurale (IBS), University of Grenoble Alpes (UGA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), F-38000 Grenoble, France.,Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.,Department of Biochemistry, Western University, London, ON, Canada.,Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway. g.a.loset@ibv.uio.no.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.,National Center for Protein Science Shanghai, Shanghai 201203, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Department of Molecular and Cell Biology, University of California, Berkeley, California.,Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA adam.renslo@ucsf.edu ychen1@health.usf.edu.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, Austin, TX, 78712, USA.,Departments of Bioengineering and Therapeutic Sciences, San Francisco, CA, 94143, USA.,Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia.,Department of Biological Chemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, MD9, Singapore.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: penchit@biotec.or.th.,Laboratoire de Chimie, UMR 5182 CNRS, École normale supérieure de Lyon, Université Lyon 1, 69364 Lyon Cedex 07, France.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, wipa@sut.ac.th.,Biomedical Sciences, Defence Science and Technology Laboratory Porton Down, SP4 0JQ Salisbury, United Kingdom.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. kleber.franchini@lnbio.cnpem.br.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Nextera AS, NO-0349 Oslo, Norway. g.a.loset@ibv.uio.no.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, Florida, USA.,York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom; fred.antson@york.ac.uk.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095; rclubb@mbi.ucla.edu ton-that.hung@uth.tmc.edu.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China.,York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854.,Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA.,Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 28 Rue du Dr. Roux, 75015, Paris, France. awilliam@pasteur.fr.,Vichem Chemie Research Ltd, Rákóczi utca 5, Veszprém, 8200, Hungary.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602; zaw@uga.edu moremen@uga.edu.,Abteilung molelukare Biowissensschaften, Molekulare Zellbiologie der Pflanzen, Goethe Universität, Frankfurt am Main, Germany.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina, 27710, USA.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, 980-8577 Sendai, Japan.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA. mmaroney@chem.umass.edu.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, USA.,the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Mechanobiology Institute, National University of Singapore, Singapore.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Medicinal Chemistry, Department of Internal Medicine, Comprehensive Cancer Center, and Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, La Habana, CP, 11300, Cuba.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A. seongminlee@austin.utexas.edu.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.,School of Chemistry, University College Dublin, Belfield, Dublin, 4, Ireland.,Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Clermont Université, Université d'Auvergne, INSERM U1071, INRA USC2018, Clermont-Ferrand, France.,Department of Chemistry, University of Georgia, Athens, GA, USA.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan; miki@kuchem.kyoto-u.ac.jp.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; Department of Biochemistry and Molecular Biology, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, 3052, Australia.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy. stefano.ciurli@unibo.it.,H3D Drug Discovery and Development Centre, Department of Drug Discovery and Development & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa; MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa. Electronic address: vinayak.singh@uct.ac.za.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8510 Kyoto, Japan.,Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7HB, UK.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Sorbonne Université, Collège doctoral, 75005, Paris, France.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia. Electronic address: r.mcgeary@uq.edu.au.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.,Institute of Biocomputation and Physics of Complex Systems (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Spain, Department of Biochemistry and Molecular and Cellular Biology, Universidad de Zaragoza, Fundacion ARAID, Gobierno de Aragon, Spain, Aragon Health Research Institute (IIS Aragon), Universidad de Zaragoza, Zaragoza, Spain.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K. jworrall@essex.ac.uk.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.,Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway. ute.krengel@kjemi.uio.no.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K. c.dong@uea.ac.uk.,Department of Medicine, University of Washington, Seattle, United States.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia m.maher@latrobe.edu.au k.truscott@latrobe.edu.au.,Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France.,From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India.,Structural Biology Research Center, VIB, Brussels, Belgium.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.,the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. howell@sickkids.ca.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan.,Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan. jysuh@snu.ac.kr.,Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.,Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America.,Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, 102-0076 Tokyo, Japan.,Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.,Departments of Bioengineering and Therapeutic Sciences, San Francisco, CA, 94143, USA; Pharmaceutical Chemistry, San Francisco, CA, 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, CA, 94143, USA.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: ubolsree@biotec.or.th.,Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Science Division, Mahidol University International College, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil.,Institute of Molecular Genetics, Russian Academy of Sciences, 123182 Moscow, Russia.,From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India pbhaumik@iitb.ac.in.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.,Department of Molecular Biosciences, Austin, TX 78712, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.,Center for Structural Genomics of Infectious Diseases, Argonne National Laboratory, Argonne, IL 60439.,Dropbox, New York, NY, USA.,Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France.,Bioss Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.,Medicinal Bioinformatics Center, Shanghai JiaoTong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, Austin, TX, 78712, USA. Electronic address: whitman@austin.utexas.edu.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France. jacqueline.cherfils@ens-paris-saclay.fr.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium.,Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100, Novara, Italy.,Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, NO-0372 Oslo, Norway.,Howard Hughes Medical Institute, University of California, Berkeley, California.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl-CoA acetyltransferase thiolase
A, B, C, D
392N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pfam DUF35
E, F, G, H
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HydroxyMethylGlutaryl-CoA synthase
I, J, K, L
349N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, I, J, K
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, D, J
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C, E, G, H, I
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
D, I, J, K, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D, F, G, H
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.617α = 90.00
b = 144.014β = 90.00
c = 230.585γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Database references
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references