6IY7

E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.

Bhakta, S.Akbar, S.Sengupta, J.

(2019) J. Mol. Biol. 431: 1426-1439

  • DOI: 10.1016/j.jmb.2019.02.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by t ...

    During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. Electronic address: tpsingh.aiims@gmail.com.,NanoTemper Technologies GmbH, Floessergasse 4, Munich, 81369, Germany.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.,Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden. julia.griese@icm.uu.se.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Institute of Biochemistry and Biotechnology, Martin-Luther-University, 06120, Halle (Saale), Germany.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA.,Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt.,Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Oxford Protein Production Facility UK, Rutherford Appleton Laboratory, Oxfordshire, UK.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Optoelectronic Information, School of Science, Qilu University of Technology, Jinan, China.,Department of Physics, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo, 171-8588, Japan.,National Joint Biomedical Engineering Research Centre on Photodynamic Technologies , Fuzhou University , Fujian 350116 , China.,Department of Microbiology and Immunology , University of Otago , Otago 9016 , New Zealand.,Center for Integrated Protein Science, Munich, Germany. hopfner@genzentrum.lmu.de.,Department of Biochemistry and Molecular Biology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, 271-8587, Japan.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.,Eli Lilly and Company, Alexandria Center for Life Sciences, New York, New York.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E 101st Street, Cleveland, OH, 44106, USA. pdk7@case.edu.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: mkkim@kaeri.re.kr.,Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, CA, 90095, USA. david@mbi.ucla.edu.,Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México.,From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and.,Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA. pdk7@case.edu.,Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA. jianglin@ucla.edu.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. yuanqp@mail.buct.edu.cn.,Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21, Solna, Sweden.,Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.,Developmental Glycobiology Section, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD, 20892-4370, USA. Kelly.Tenhagen@nih.gov.,Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA. jprose@uga.edu.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. stefan.raunser@mpi-dortmund.mpg.de.,School of Cellular and Molecular Medicine, University of Bristol, UK.,Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA fwb4@cdc.gov.,California Nano Systems Institute, UCLA, Los Angeles, CA, 90095, USA. hong.zhou@ucla.edu.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. cedric.leyrat@igf.cnrs.fr.,Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.,Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.,Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California.,From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom mw240@cam.ac.uk.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.,Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.,Department of Natural Product Biochemistry, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. harrison@crystal.harvard.edu.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.,Department of Chemistry, University of Oxford, UK.,Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. hogbom@dbb.su.se.,Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden.,Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, CA, 90095, USA.,School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada.,Department of Rheumatology & Clinical Immunology, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands.,Eli Lilly and Company, Indianapolis, Indiana.,Section on Biological Chemistry, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD, 20892-4370, USA.,Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China.,Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki, 852-8588, Japan.,Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: saylim@kaeri.re.kr.,Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11973, USA.,Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. julia.griese@icm.uu.se.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.,Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China.,CBS, University of Montpellier, CNRS, INSERM, Montpellier, 34090, France.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. yuanqp@mail.buct.edu.cn.,Graduate School of Medicine , University of Wollongong , Wollongong , NSW 2522 , Australia.,the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada kalle.gehring@mcgill.ca.,Institute of Infection and Immunity, Cardiff University, UK.,Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India. Electronic address: jayati@iicb.res.in.,Developmental Glycobiology Section, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD, 20892-4370, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, USA. pdk7@case.edu.,Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.,Eli Lilly and Company, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. sebastien.granier@igf.cnrs.fr.,California Nano Systems Institute, UCLA, Los Angeles, CA, 90095, USA.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Chemistry, Fudan University, Shanghai, China.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. martin.ott@dbb.su.se.,Institute of Molecular Biology and Pathology, CNR, Rome, Italy.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: tatiana.kutateladze@ucdenver.edu.,Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Pancreatic Research Group, South Western Sydney Clinical School , University of New South Wales, and Ingham Institute for Applied Medical Research , Liverpool , NSW 2170 , Australia.,Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA.,Department of Functional Bioscience, Infection Biology, Fukuoka Dental College, Matsudo, Tamura, Sawara, Fukuoka, 814-0913, Japan.,National Center for Protein Science, Shanghai, China.,Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.,From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China.,Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland.,Eli Lilly and Company, Lilly Research Laboratories, Avenida de la Industria, Alcobendas, Spain.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA. hong.zhou@ucla.edu.,School of Chemistry, University of Nottingham, Nottingham, United Kingdom.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. matthias.schmidt@uni-ulm.de.,Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China.,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA bnolen@uoregon.edu.,Key Laboratory of Structural Biology , Chinese Academy of Sciences , Hefei , Anhui 230026 , China.,School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA. yajunyan@uga.edu.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. Electronic address: yinyuxin@hsc.pku.edu.cn.,Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. marcus.faendrich@uni-ulm.de.,Department of Medical Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, D.F, Mexico City, 07320, Mexico.,Department of Microbiology and Oral Infection, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki, 852-8588, Japan.,Tri-Institutional PhD Program in Chemical Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel. Electronic address: noam@ch.technion.ac.il.,Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106-4988, USA.,Department of Medical Cell Biology, Uppsala University, SE-75123, Uppsala, Sweden.,Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China.,Eli Lilly and Company, Indianapolis, Indiana. buchananse@lilly.com.,Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
P
169Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: def (fms)
EC: 3.5.1.88
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6K3
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific & Industrial ResearchIndia--
Department of Science & Technology (India)IndiaSB/SO/BB-0025/2014

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Structure summary