6E4R

Crystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl Transferase PGANT9B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.061 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A molecular switch orchestrates enzyme specificity and secretory granule morphology.

Ji, S.Samara, N.L.Revoredo, L.Zhang, L.Tran, D.T.Muirhead, K.Tabak, L.A.Ten Hagen, K.G.

(2018) Nat Commun 9: 3508-3508

  • DOI: 10.1038/s41467-018-05978-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulated secretion is an essential process where molecules destined for export are directed to membranous secretory granules, where they undergo packaging and maturation. Here, we identify a gene (pgant9) that influences the structure and shape of s ...

    Regulated secretion is an essential process where molecules destined for export are directed to membranous secretory granules, where they undergo packaging and maturation. Here, we identify a gene (pgant9) that influences the structure and shape of secretory granules within the Drosophila salivary gland. Loss of pgant9, which encodes an O-glycosyltransferase, results in secretory granules with an irregular, shard-like morphology, and altered glycosylation of cargo. Interestingly, pgant9 undergoes a splicing event that acts as a molecular switch to alter the charge of a loop controlling access to the active site of the enzyme. The splice variant with the negatively charged loop glycosylates the positively charged secretory cargo and rescues secretory granule morphology. Our study highlights a mechanism for dictating substrate specificity within the O-glycosyltransferase enzyme family. Moreover, our in vitro and in vivo studies suggest that the glycosylation status of secretory cargo influences the morphology of maturing secretory granules.


    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 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.,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.,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.,Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,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.,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.,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.,Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA fwb4@cdc.gov.,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.,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 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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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
polypeptide N-acetylgalactosaminyltransferase 9
A, B
507Drosophila melanogasterMutation(s): 0 
Gene Names: Pgant9
EC: 2.4.1.41
Find proteins for Q8MRC9 (Drosophila melanogaster)
Go to UniProtKB:  Q8MRC9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.061 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.913α = 90.00
b = 48.440β = 91.40
c = 232.037γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release