6OM4

The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by theN-formyl of the peptide precursor.

Dong, S.H.Kulikovsky, A.Zukher, I.Estrada, P.Dubiley, S.Severinov, K.Nair, S.K.

(2019) Chem Sci 10: 2391-2395

  • DOI: 10.1039/c8sc03173h

  • PubMed Abstract: 
  • Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP <i>via </i> a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which ...

    Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N-P linkage. We demonstrate that MccB only efficiently processes the precursor heptapeptide that retains the N -formylated initiator Met (fMet). Binding studies and kinetic measurements evidence the role of the N -formyl moiety. Structural data show that the N -formyl peptide binding results in an ordering of residues in the MccB "crossover loop", which dictates specificity in homologous ubiquitin activating enzymes. The N -formyl peptide exhibits substrate inhibition, and cannot be displaced from MccB by the desformyl counterpart. Such substrate inhibition may be a strategy to avert unwanted McC buildup and avert toxicity in the cytoplasm of producing organisms.


    Organizational Affiliation

    Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK.,Center for Drug Discovery, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.,Institute of Biochemistry, ETH Zurich, Zurich, Switzerland. volodymyr.korkhov@psi.ch.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address: ervin.fodor@path.ox.ac.uk.,School of Biochemistry and Immunology, Trinity College Dublin, Dublin, 2, Ireland.,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.,Synchrotron Radiation Research Section of MCL, National Cancer Institute, S Cass Ave 9700, Argonne, IL, U.S.A. milosz.ruszkowski@nih.gov.,Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Illinois , USA.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.,X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China.,School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China. liu-lab@vip.163.com.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch , National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States.,University of Pavia, Department of Molecular Medicine, Human Physiology Unit, Via Forlanini 6, I-27100, Pavia, Italy.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and alan.cartmell2@newcastle.ac.uk.,School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.,Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy.,JEM Utilization Center, Human Spaceflight Technology Directorate , Japan Aerospace Exploration Agency (JAXA) , 2-1-1 Sengen , Tsukuba-shi , Ibaraki 305-8505 , Japan.,Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA.,School of Medicine, Tsinghua University, Beijing, 100084, China.,Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain. Electronic address: adoracion.gomez@uam.es.,Center for Structural Biology, and.,Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland ausra.domanska@helsinki.fi sarah.butcher@helsinki.fi.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,Living Systems Institute, University of Exeter, Exeter, UK.,Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A. adha@ufl.edu.,School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden; adnane.achour@ki.se T.van_Hall@lumc.nl.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. nyasui@okayama-u.ac.jp.,State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000, China.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064 harry@nuvolari.ucsc.edu.,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA.,Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,New York Structural Biology Center, New York, NY, USA.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA. Electronic address: pabeal@ucdavis.edu.,Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,Center for Life Sciences , Skolkov Institute of Science and Technology , 3 Nobel str. , 143026 Moscow , Russia.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: liuzhj@shanghaitech.edu.cn.,Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Canada.,CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: mko2@cdc.gov.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden.,University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200, Copenhagen N, Denmark. pontus@sund.ku.dk.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.,a Molecular Cancer Research Group, Department of Medical Biology , University of Tromsø -The Arctic University of Norway , Tromsø , Norway.,Department of Pharmacy, Dongguk University, Goyang 10326, Korea.,Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea.,Department of Chemistry, Portland State University, Portland, OR, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.,School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PRC.,Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045.,Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.,Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.,Departments of Infectious Diseases and Hematology , Kumamoto University Graduate School of Biomedical Sciences , Kumamoto 860-8556 , Japan.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and jcordero@uthsc.edu.,Howard Hughes Medical Institute, Chevy Chase, United States.,Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand brian.monk@otago.ac.nz.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC.,MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Aquaporin A/S, Nymøllevej 78, DK-2800, Lyngby, Denmark.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen 361102, P.R. China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; adnane.achour@ki.se T.van_Hall@lumc.nl.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China. Electronic address: wmxing@sibs.ac.cn.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: kasper.rand@sund.ku.dk.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, PRC.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,Department of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200433, China.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark.,Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720; view@berkeley.edu monica.balsera@csic.es.,Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402.,Department of Biological Chemistry and Pharmacology , The Ohio State University , Columbus , Ohio 43210 , United States.,d Peptide Chemistry Science Technology Platform , The Francis Crick Institute , London , UK.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Department of Chemistry, University of Florida, Gainesville, FL, U.S.A.,Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland. Electronic address: s.rodziewicz-motowidlo@ug.edu.pl.,Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.,Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA.,Department of Physics, Ohio State University, Columbus, OH 43210.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China. Electronic address: wangyc@njau.edu.cn.,Technical University of Denmark, Department of Environmental Engineering, Bygningstorvet Building 115, DK-2800 Kgs, Lyngby, Denmark.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2880, Denmark.,Department of Molecular Physiology and Biophysics.,Department of Chemistry, School of Physical Sciences, University of Liverpool, UK.,Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, 2000 Neuchâtel, Switzerland.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC. Electronic address: gaon@pku.edu.cn.,Department of Biology, Technische Universität Darmstadt, D64287 Darmstadt, Germany.,Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,School of Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.,Waksman Institute for Microbiology , 190 Frelinghuysen Road , Piscataway , New Jersey , USA . Email: severik@waksman.rutgers.edu.,Department of Biochemistry and Molecular Biology and ‡Department of Immunology, Mayo Clinic , Rochester, Minnesota 55905, United States.,Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Daejeon, South Korea.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Pharmaceutical Chemistry and Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, KS, USA.,Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. Electronic address: luigi.messori@unifi.it.,The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA vprasad@bcm.edu.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.,Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnologico de Bizkaia, Derio, Spain.,School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC. Electronic address: jinqi@ipbcams.ac.cn.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA Hong.Zhou@UCLA.edu.,Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: leila@chem.ku.dk.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.,Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale, Università di Parma and INSTM UdR Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Graduate School of Medical Science and Engineering, College of Life Science and Bioengineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,c Molecular Cell Biology of Autophagy Laboratory , The Francis Crick Institute , London , UK.,School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; Core Research for Evolutional Science and Technology(CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan. Electronic address: hig@sci.u-hyogo.ac.jp.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA. Electronic address: aihar001@umn.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA.,Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, 37007 Salamanca, Spain.,Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milan, 20133 Milan, Italy.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA; Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States.,Lund University, Department of Experimental Medical Science, Sölvegatan 19, SE-221 84, Lund, Sweden. pontus@sund.ku.dk.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.,University of Copenhagen, Department of Biology, Universitetsparken 13, DK-2100, Copenhagen OE, Denmark.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States.,Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany schwalbe@nmr.uni-frankfurt.de.,Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, 37008 Salamanca, Spain view@berkeley.edu monica.balsera@csic.es.,Department of Chemistry, Portland State University, Portland, OR, USA. reichow@pdx.edu.,Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.,b Structural Biology , The Francis Crick Institute , London , UK.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK.,Novartis Institutes for Biomedical Research (China), Zhangjiang Hi-Tech Park , Pudong New Area, Shanghai 201203, China.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK. Electronic address: jonathan@strubi.ox.ac.uk.,Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,School of Pharmacy, University of Otago, Dunedin, New Zealand.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.,Universidade de Lisboa, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . Email: snair@illinois.edu.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK.,Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; NanoBioMedical Center, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: erica@scripps.edu.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. Electronic address: gcdu@jiangnan.edu.cn.,Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,Centro Universitario de la Defensa, Ctra. Huesca s/n, 50090 Zaragoza, Spain.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Department of Pathology, The University of Chicago, Chicago, IL, United States.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi, 13, 56124 Pisa, Italy; Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Cell Therapy Institute, Nova Southeastern University, Fort Lauderdale, FL 33314; and.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.,X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA.,Department of Bioengineering and Therapeutic Science , University of California, San Francisco , San Francisco , California 94158 , United States.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045; tatiana.kutateladze@ucdenver.edu.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.,Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246, Université Claude Bernard, Bâtiment Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France. Yves.queneau@insa-lyon.fr.,Department of Molecular Physiology and Biophysics, terunaga.nakagawa@vanderbilt.edu.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain.,Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,Campus Chemical Instrument Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Institute of Biochemistry, University of Zurich, Zurich, Switzerland.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Committee on Microbiology, The University of Chicago, Chicago, IL, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093.,Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom; n.le-brun@uea.ac.uk.,College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Univ. Grenoble Alpes, CNRS, CEA , INAC-SyMMES , 38000 Grenoble , France.,Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,University of Chinese Academy of Sciences, Beijing, China.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and.,Department of Food and Nutrition, Duksung Women's University, Seoul, South Korea.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Umeå Center for Microbial Research, Umeå University, Umeå, Sweden.,Department of Chemistry , University of California, Davis , Davis , California 95695 , United States.,Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA.,Carl Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Illinois , USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,DiscoveRx Corporation , Fremont, California 94538, United States.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,School of Life Sciences, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,University of Copenhagen, Department of Biology, Universitetsparken 13, DK-2100, Copenhagen OE, Denmark. papedersen@bio.ku.dk.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain. Electronic address: pereda@usal.es.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Department of Biology, Molecular Basis of Disease , Georgia State University , Atlanta , Georgia 30303 , United States.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Department of Refractory Viral Infections , National Center for Global Health and Medicine Research Institute , Tokyo 162-8655 , Japan.,Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.,School of Medicine, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,School of Medicine, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre , 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093-0378, USA.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. a_yama@cc.okayama-u.ac.jp.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402. liu-lab@vip.163.com.,Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A.,University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland xiad@mail.nih.gov.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MccB protein
A, B
348Escherichia coliMutation(s): 0 
Gene Names: mccB
Find proteins for Q47506 (Escherichia coli)
Go to UniProtKB:  Q47506
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Microcin C7
C, D
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ND7
Query on ND7

Download SDF File 
Download CCD File 
C, D
5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
C10 H15 N6 O6 P
LDEMREUBLBGZBO-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, D
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.094α = 90.00
b = 76.059β = 90.00
c = 131.902γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXmodel building
XDSdata scaling
XDSdata reduction
BUCCANEERmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI117210

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release