6N96

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.

Stunkard, L.M.Dixon, A.D.Huth, T.J.Lohman, J.R.

(2019) J. Am. Chem. Soc. 141: 5121-5124

  • DOI: 10.1021/jacs.9b00650
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malonyl-thioesters are reactive centers of malonyl-CoA and malonyl- S-acyl carrier protein, essential to fatty acid, polyketide and various specialized metabolite biosynthesis. Enzymes that create or use malonyl-thioesters spontaneously hydrolyze or ...

    Malonyl-thioesters are reactive centers of malonyl-CoA and malonyl- S-acyl carrier protein, essential to fatty acid, polyketide and various specialized metabolite biosynthesis. Enzymes that create or use malonyl-thioesters spontaneously hydrolyze or decarboxylate reactants on the crystallographic time frame preventing determination of structure-function relationships. To address this problem, we have synthesized a panel of methylmalonyl-CoA analogs with the carboxylate represented by a sulfonate or nitro and the thioester retained or represented by an ester or amide. Structures of Escherichia coli methylmalonyl-CoA decarboxylase in complex with our analogs affords insight into substrate binding and the catalytic mechanism. Counterintuitively, the negatively charged sulfonate and nitronate functional groups of our analogs bind in an active site hydrophobic pocket. Upon decarboxylation the enolate intermediate is protonated by a histidine preventing CO 2 -enolate recombination, yielding propionyl-CoA. Activity assays support a histidine catalytic acid and reveal the enzyme displays significant hydrolysis activity. Our structures also provide insight into this hydrolysis activity. Our analogs inhibit decarboxylation/hydrolysis activity with low micromolar K i values. This study sets precedents for using malonyl-CoA analogs with carboxyate isosteres to study the complicated structure-function relationships of acyl-CoA carboxylases, trans-carboxytransferases, malonyltransferases and β-ketoacylsynthases.


    Organizational Affiliation

    Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Research Institute for Interdisciplinary Science, Okayama University, 700-8530 Okayama, Japan.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.,National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand.,Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom. Electronic address: mh256@cam.ac.uk.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy. emilio.parisini@iit.it.,From the Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States.,Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.,Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen, Erlangen, Germany.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.,Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark. premo@dtu.dk.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas, 77030, USA.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China; suisf@mail.tsinghua.edu.cn shen@cc.okayama-u.ac.jp.,College of Chemistry, Beijing Normal University, Beijing, 100875, China.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium han.remaut@vub.be.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA bgraham@nih.gov.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, China; jacobsen@ucla.edu jmdu@sibs.ac.cn.,CAS Center for Excellence in Biomacromolecules, Beijing 100101, China.,The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.,Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan hiroaki.mitsuya2@nih.gov.,Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.,Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan. nureki@bs.s.u-tokyo.ac.jp.,Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA.,Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. kahne@chemistry.harvard.edu.,Astex Pharmaceuticals, Cambridge, United Kingdom.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.,INSERM, U1108, Paris, France.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Edgewood Chemical Biological Center, United States Army , Aberdeen Proving Ground, Aberdeen , Maryland 21010 , United States.,Max Planck Institute of Biochemistry , 82152 Martinsried , Germany.,Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Department of Biophysics, Bose Institute, Kolkata, 700054, India.,Institute of Oceanography, Minjiang University, 350108 Fuzhou, China.,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Biology, New York University, New York, NY 10003.,Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada. jia@queensu.ca.,Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway. premo@dtu.dk.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Array BioPharma, Inc., 3200 Walnut Street, Boulder, Colorado 80301, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. andrew_kruse@hms.harvard.edu.,Laboratory Molecular and Cellular Signaling, Department Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I Bus 802, Herestraat 49 3000 Leuven, Belgium.,Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan.,University of Chinese Academy of Sciences, Beijing 100049, China.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,School of Nanoscience and Technology, IIT Kharagpur, Kharagpur, 721302, India. Electronic address: anupam.midya@iitkgp.ac.in.,School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom.,Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,D3-PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,University of Chinese Academy of Sciences , No. 19 Yuquan Road , Beijing 100049 , China.,Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China.,Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. janschu@biochem.mpg.de gkurisu@protein.osaka-u.ac.jp marc.m.nowaczyk@rub.de.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China; suisf@mail.tsinghua.edu.cn shen@cc.okayama-u.ac.jp.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Institute for Genetics, University of Cologne, Cologne, Germany.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom. Electronic address: fh111@cam.ac.uk.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.,Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei-shi, Tokyo, 184-8584, Japan.,Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany. janschu@biochem.mpg.de gkurisu@protein.osaka-u.ac.jp marc.m.nowaczyk@rub.de.,Department of Pharmacology, Howard Hughes Medical Institute.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.,University of Lübeck , 23562 Lübeck , Germany.,School of Nanoscience and Technology, IIT Kharagpur, Kharagpur, 721302, India.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Biology Department, Brookhaven National Laboratory, Upton, NY 11793.,Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada brian.mark@umanitoba.ca.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, 8000, Aarhus, Denmark.,Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. Electronic address: yesheng@ibp.ac.cn.,Institute of Anatomy, Medical Faculty, University of Duisburg-Essen, Essen, Germany.,Department of Physics, IIT Kharagpur, Kharagpur, 721302, India.,From the Department of Chemistry and Biochemistry, rclubb@mbi.ucla.edu.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , China.,School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; daniel.wilson@chemie.uni-hamburg.de.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032; wah2@cumc.columbia.edu yuhang.chen@genetics.ac.cn.,Nano Medical Engineering Laboratory, RIKEN Cluster of Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Graduate School Materials Science in Mainz, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128, Mainz, Germany.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. janschu@biochem.mpg.de gkurisu@protein.osaka-u.ac.jp marc.m.nowaczyk@rub.de.,School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA.,Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA. Electronic address: mq2102@cumc.columbia.edu.,RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,College of Chemistry, Beijing Normal University, Beijing, 100875, China. jimin_z@bnu.edu.cn.,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095.,the Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Helmholtz Centre for Infection Research , 38124 Braunschweig , Germany.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. Electronic address: tpsingh.aiims@gmail.com.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.,Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055 Guangdong, China.,Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, IL 60439, USA.,School of Biological Sciences , Nanyang Technological University , 639798 Singapore.,Departments of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, United States.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy. alfonso.gautieri@polimi.it.,Daiichi Sankyo Deutschland GmbH, Zielstattstr. 48, 81379 München, Germany.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.,Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan tanaka.hiroshi@chugai-pharm.co.jp.,Mirati Therapeutics, Inc., 9393 Towne Centre Drive, Suite 200, San Diego, California 92121, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. kahne@chemistry.harvard.edu.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; andrew_kruse@hms.harvard.edu.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy.,Manufacturing, Commonwealth Scientific and Industrial Research Organization (CSIRO) , Clayton , Vic 3168 , Australia.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.,Department of Biophysics, Bose Institute, Kolkata, 700054, India. Electronic address: bhunia@jcbose.ac.in.,Institute for Experimental Medical Research, Oslo University Hospital, 0424, Oslo, Norway. premo@dtu.dk.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmaceutical and Biomedical Sciences , University of Georgia , Athens , Georgia 30602 , United States.,Department of Biotechnology, IIT Madras, Chennai, 600036, India.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China syf@mail.hzau.edu.cn.,Neuroscience Graduate Program, Brown University, Providence, RI, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, United States.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; wah2@cumc.columbia.edu yuhang.chen@genetics.ac.cn.,Department of Biology and Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,School of Life Science , Huizhou University , Huizhou 516007 , China.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Technical University Darmstadt , Alarich-Weiss-Straße 4 , 64287 Darmstadt , Germany.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology and Immunology, National University of Singapore, 117545 Singapore.,New York Structural Biology Center , New York , New York 10027 , United States.,National Institute of Biological Sciences, Beijing, China.,UCLA-DOE Institute of Genomics and Proteomics and.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada. jr.min@utoronto.ca.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany goerlich@mpibpc.mpg.de.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095; jacobsen@ucla.edu jmdu@sibs.ac.cn.,Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.,Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA nicolas_fawzi@brown.edu.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Institute of Immunology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany.,AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.,Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany g.hansman@dkfz.de.,the Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902.,Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.,Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.,Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Observatory , 7925 Cape Town , Republic of South Africa.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China. dhlin@xmu.edu.cn.,Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.,German Center for Infection Research, Partner Site Munich, Munich, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan. t-2438@bs.s.u-tokyo.ac.jp.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Division of Viral Disease, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Molecular Biology Institute, UCLA, Los Angeles, California 90095.,Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, 100-0004, Japan.,Division of Molecular Medicine, Bose Institute, Kolkata, 700054, India.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.,Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,From the Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, shen@cc.okayama-u.ac.jp.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. simonasm@mrc-lmb.cam.ac.uk.,Graduate School of Natural Science and Technology, Okayama University, 700-8530 Okayama, Japan.,Department of Pharmacology and Molecular Therapeutics, Uniformed Services University, Bethesda, MD, USA.,School of Chemistry, National University of Ireland, University Road, Galway, Ireland.,Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,School of Biological Sciences & Maurice Wilkins Centre , University of Auckland , Auckland 1010 , New Zealand.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 90187 Umeå, Sweden.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences ; Guangzhou Medical University, Guangzhou 510530 , China.,Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Experimental Retrovilogy Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,School of Pharmaceutical Sciences , Jilin University , No.1266 Fujin Road , Chaoyang District, Changchun , Jilin 130021 , China.,Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. Electronic address: amaejima@mail.ecc.u-tokyo.ac.jp.,Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States.,Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.,IMED Oncology, AstraZeneca, Waltham, Massachusetts 02451, USA. neil.grimster@astrazeneca.com.,Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,the Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, and.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Department of Biochemistry and Cellular Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.,From the Department of Chemistry and Biochemistry.,Structural Genomics Consortium, University of Toronto , 101 College Street, Toronto, ON M5G 1L7, Canada.,University of Chinese Academy of Sciences, 100049 Beijing, China.,Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.,Imevax GmbH, Munich, Germany.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA. Electronic address: lei.shi2@nih.gov.,Chemical Sciences Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8391, Gaithersburg, MD 20899-8391, USA.,Department of Pharmacy, Uppsala University, SE-75232, Uppsala, Sweden; Department of Pharmacy, University of Copenhagen, DK-2100, Copenhagen, Denmark. Electronic address: martin.malmsten@farmaci.uu.se.,Department of Microbiology, The Ohio State University, Columbus, OH, USA. ruiz.82@osu.edu.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway. michele.cascella@kjemi.uio.no.,Technische Universität Braunschweig , 38106 Braunschweig , Germany.,Department of Pharmacology, Howard Hughes Medical Institute. Electronic address: hongtao.yu@utsouthwestern.edu.,Ipsen Bioinnovation Limited, Abingdon, United Kingdom.,Astex Pharmaceuticals, Cambridge, United Kingdom. George.ward@astx.com.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, China.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas, 77030, USA. mglee@mdanderson.org.,Pasteur Institute, Viral Pathogenesis Unit, Paris, France.,Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.,Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. jr.min@utoronto.ca.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China. Electronic address: rzhang@ibp.ac.cn.,Virus Ecology Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL) , Guangzhou 510530 , China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Saelands vei 26, 0371, Oslo, Norway. michele.cascella@kjemi.uio.no.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylmalonyl-CoA decarboxylase
A, B, C, D, E, F
261Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: scpB (mmcD, ygfG)
EC: 4.1.1.-
Find proteins for P52045 (Escherichia coli (strain K12))
Go to UniProtKB:  P52045
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO5
Query on SO5

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid
C24 H40 N7 O21 P3 S
BEMUOEZGNHFKKE-AGCMQPJKSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
LCV
Query on LCV

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid
C24 H40 N7 O21 P3 S
BEMUOEZGNHFKKE-IBNUZSNCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.148α = 90.00
b = 114.660β = 90.00
c = 192.705γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release