6MP7

Crystal structure of the E257A mutant of BlMan5B in complex with GlcNAc (soaking)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist beta-Mannosidase.

Pirolla, R.A.S.Persinoti, G.F.Gozzo, F.C.de Giuseppe, P.O.Murakami, M.T.Cordeiro, R.L.

(2019) J. Mol. Biol. 431: 732-747

  • DOI: 10.1016/j.jmb.2018.12.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bifidobacteria represent one of the first colonizers of human gut microbiota, providing to this ecosystem better health and nutrition. To maintain a mutualistic relationship, they have enzymes to degrade and use complex carbohydrates non-digestible b ...

    Bifidobacteria represent one of the first colonizers of human gut microbiota, providing to this ecosystem better health and nutrition. To maintain a mutualistic relationship, they have enzymes to degrade and use complex carbohydrates non-digestible by their hosts. To succeed in the densely populated gut environment, they evolved molecular strategies that remain poorly understood. Herein, we report a novel mechanism found in probiotic Bifidobacteria for the depolymerization of the ubiquitous 2-acetamido-2-deoxy-4-O-(β-d-mannopyranosyl)-d-glucopyranose (Man-β-1,4-GlcNAc), a disaccharide that composes the universal core of eukaryotic N-glycans. In contrast to Bacteroidetes, these Bifidobacteria have a specialist and strain-specific β-mannosidase that contains three distinctive structural elements conferring high selectivity for Man-β-1,4-GlcNAc: a lid that undergoes conformational changes upon substrate binding, a tryptophan residue swapped between the two dimeric subunits to accommodate the GlcNAc moiety, and a Rossmann fold subdomain strategically located near to the active site pocket. These key structural elements for Man-β-1,4-GlcNAc specificity are highly conserved in Bifidobacterium species adapted to the gut of a wide range of social animals, including bee, pig, rabbit, and human. Together, our findings uncover an unprecedented molecular strategy employed by Bifidobacteria to selectively uptake carbohydrates from N-glycans in social hosts.


    Organizational Affiliation

    Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: amy.howell@uconn.edu.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan. narita.akihiro@f.mbox.nagoya-u.ac.jp.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto, 610-0394, Japan.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA. Electronic address: marzena.pazgier@usuhs.edu.,Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, SP, Brazil.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: steven.porcelli@einstein.yu.edu.,Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, 92093.,Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663, Kaiserslautern, Germany.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi, 480-1192, Japan.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany. ulrich.ermler@biophys.mpg.de.,Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: mario.murakami@ctbe.cnpem.br.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. Electronic address: zhaole2@mail.xjtu.edu.cn.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,PhD Program in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal.,Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany.,Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia.,Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. adha@ufl.edu.,CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,From the High Pressure and Synchrotron Radiation Physics Division and ravimakde@rrcat.gov.in.,Institute for Interdisciplinary Research (IIIC), University of Coimbra, 3030-789 Coimbra, Portugal.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany. U.Rau@tu-bs.de.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging at the University of Melbourne, Melbourne, Australia.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. koss@bsd.uchicago.edu.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany. matthias.boll@biologie.uni-freiburg.de.,Key Laboratory of Fermentation Engineering, Ministry of Education, College of Bioengineering, Hubei University of Technology, Wuhan, China; Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,AstraZeneca R&D, Darwin Building Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Korea.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel; The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan 52900, Israel. Electronic address: yanay@ofranlab.org.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States.,Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India and snjam@barc.gov.in.,Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. yok5@snu.ac.kr.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Millennium Institute on Immunology and Immunotherapy, Programa de Inmunologia, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Korea.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Computational Biochemistry, University of Bayreuth, Universitätsstrasse 30, NW I, 95447, Bayreuth, Germany.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,RIKEN, SPring-8 Center, Hyogo, Japan.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil; Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,University of Chinese Academy of Sciences, Beijing, China.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,From the High Pressure and Synchrotron Radiation Physics Division and.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.,School of Biochemistry, Devi Ahilya University, Indore 452001, India.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK. s.helaine@imperial.ac.uk.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA. bruner@chem.ufl.edu.,National Institute for Research in Tuberculosis, Chennai 600031, India.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. ss1@nih.gov.,Biophysics, Department of Physics, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany.,Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA.,Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. eric.xu@vai.org.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. ss1@nih.gov.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel.,Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, United States.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Faculty of Health and Welfare, Tokai Gakuin University, Nakakirino-cyo 5-68, Kakamigahara, Gifu, 504-8511, Japan.,Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK.,Biochemistry Department, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia. Electronic address: jerome.lenours@monash.edu.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. koss@bsd.uchicago.edu.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA. eric.xu@vai.org.,Department of Chemistry, University of California, San Diego, La Jolla, California, 92093.,Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: priscila.giuseppe@ctbe.cnpem.br.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Protech Inc., Yongeon 103 Daehangno, Jongno-gu, Seoul, 110-799, Republic of Korea. yok5@snu.ac.kr.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: mrn@iisc.ac.in.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BlMan5B
A, B
449Bifidobacterium longum (strain DJO10A)Mutation(s): 1 
Find proteins for B3DQP5 (Bifidobacterium longum (strain DJO10A))
Go to UniProtKB:  B3DQP5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 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: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.805α = 90.00
b = 101.247β = 90.00
c = 172.935γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil2015/26982-0
Sao Paulo Research FoundationBrazil2016/00740-2

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references