6HZF

BP0997, GH138 enzyme targeting pectin rhamnogalacturonan II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and functional analyses of glycoside hydrolase 138 enzymes targeting chain A galacturonic acid in the complex pectin rhamnogalacturonan II.

Labourel, A.Basle, A.Munoz-Munoz, J.Ndeh, D.Booth, S.Nepogodiev, S.A.Field, R.A.Cartmell, A.

(2019) J.Biol.Chem. 294: 7711-7721

  • DOI: 10.1074/jbc.RA118.006626
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiome. The selection pressures in this environment have spurred the evolution of a complex reservoir of microbial genes encoding carbohydrate-active enzymes (CAZ ...

    The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiome. The selection pressures in this environment have spurred the evolution of a complex reservoir of microbial genes encoding carbohydrate-active enzymes (CAZymes). Previously, we have shown that the human gut bacterium Bacteroides thetaiotaomicron ( Bt ) can depolymerize the most structurally complex glycan, the plant pectin rhamnogalacturonan II (RGII), commonly found in the human diet. Previous investigation of the RGII-degrading apparatus in Bt identified BT0997 as a new CAZyme family, classified as glycoside hydrolase 138 (GH138). The mechanism of substrate recognition by GH138, however, remains unclear. Here, using synthetic substrates and biochemical assays, we show that BT0997 targets the d-galacturonic acid-α-1,2-l-rhamnose linkage in chain A of RGII and that it absolutely requires the presence of a second d-galacturonic acid side chain (linked β-1,3 to l-rhamnose) for activity. NMR analysis revealed that BT0997 operates through a double displacement retaining mechanism. We also report the crystal structure of a BT0997 homolog, BPA0997 from Bacteroides paurosaccharolyticus , in complex with ligands at 1.6 Å resolution. The structure disclosed that the enzyme comprises four domains, including a catalytic TIM (α/β) 8 barrel. Characterization of several BT0997 variants identified Glu-294 and Glu-361 as the catalytic acid/base and nucleophile, respectively, and we observed a chloride ion close to the active site. The three-dimensional structure and bioinformatic analysis revealed that two arginines, Arg-332 and Arg-521, are key specificity determinants of BT0997 in targeting d-galacturonic acid residues. In summary, our study reports the first structural and mechanistic analyses of GH138 enzymes.


    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.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,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.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.,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.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Graduate School of Medical Science and Engineering, College of Life Science and Bioengineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,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.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA.,Center for Structural Biology, and.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,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.,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.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 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.,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.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: liuzhj@shanghaitech.edu.cn.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045.,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.,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.,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.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,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 Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045; tatiana.kutateladze@ucdenver.edu.,MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.,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.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Department of Molecular Physiology and Biophysics, terunaga.nakagawa@vanderbilt.edu.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,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.,Campus Chemical Instrument Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Biological Chemistry and Pharmacology , The Ohio State University , Columbus , Ohio 43210 , United States.,Committee on Microbiology, The University of Chicago, Chicago, IL, United States.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,University of Chinese Academy of Sciences, Beijing, China.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,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.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,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.,Umeå Center for Microbial Research, Umeå University, Umeå, Sweden.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Department of Chemistry, Umeå University, Umeå, Sweden.,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 Physics, Ohio State University, Columbus, OH 43210.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,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.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,Department of Molecular Physiology and Biophysics.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,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.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.,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.,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 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.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BPa0997
A
893N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BPa0997
B
871N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A, B
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.785α = 90.00
b = 106.207β = 99.44
c = 138.504γ = 90.00
Software Package:
Software NamePurpose
BUCCANEERmodel building
XDSdata reduction
ARP/wARPmodel building
Cootmodel building
HKL2Mapphasing
REFMACrefinement
SHELXDEphasing
Aimlessdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322820

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references
  • Version 1.2: 2019-05-22
    Type: Data collection, Database references