5D00

Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Structural, Functional, and Computational Analysis of BshA, the First Enzyme in the Bacillithiol Biosynthesis Pathway.

Winchell, K.R.Egeler, P.W.VanDuinen, A.J.Jackson, L.B.Karpen, M.E.Cook, P.D.

(2016) Biochemistry 55: 4654-4665

  • DOI: 10.1021/acs.biochem.6b00472
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive ox ...

    Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive oxygen species and harmful xenobiotic agents, including the antibiotic fosfomycin. BshA, BshB, and BshC are the enzymes involved in bacillithiol biosynthesis. BshA is a retaining glycosyltransferase responsible for the first committed step in bacillithiol production, namely the addition of N-acetylglucosamine to l-malate. Retaining glycosyltransferases like BshA are proposed to utilize an SNi-like reaction mechanism in which leaving group departure and nucleophilic attack occur on the same face of the hexose. However, significant questions regarding the details of how BshA and similar enzymes accommodate their substrates and facilitate catalysis persist. Here we report X-ray crystallographic structures of BshA from Bacillus subtilis 168 bound with UMP and/or GlcNAc-mal at resolutions of 2.15 and 2.02 Å, respectively. These ligand-bound structures, along with our functional and computational studies, provide clearer insight into how BshA and other retaining GT-B glycosyltransferases operate, corroborating the substrate-assisted, SNi-like reaction mechanism. The analyses presented herein can serve as the basis for the design of inhibitors capable of preventing bacillithiol production and, subsequently, help combat resistance to fosfomycin in various pathogenic Gram-positive microorganisms.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5G 1L6, Canada.,Microbiology and Biotechnology, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609 Hamburg, Germany.,a State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemistry, Grand Valley State University , Allendale, Michigan 49401, United States.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA. Electronic address: bjorkman@caltech.edu.,University of Florence , Department of Chemistry "Ugo Schiff" , Via della Lastruccia 3 , 50019 Sesto Fiorentino ( Florence ), Italy.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and hejianhua@sinap.ac.cn.,Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA.,Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao, Shandong 266101, China. cuiqiu@qibebt.ac.cn fengyg@qibebt.ac.cn.,JAN Scientific Inc., Seattle, WA 98105.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.,Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,the Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.,Molecular Biology of Microbial Consortia, University of Hamburg, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609, Hamburg, Germany.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico.,Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: jxqi@im.ac.cn.,From the Department of Biochemistry.,Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.,College of Pharmacy, Pusan National University, Busandaehak-ro, Pusan 46241, Republic of Korea.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA. Electronic address: glander@scripps.edu.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark. Electronic address: leila@chem.ku.dk.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. Electronic address: bwiedenheft@gmail.com.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.,the Polymer Chemistry Group, Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan, and.,Department of Cell and Molecular Biology, Grand Valley State University , Allendale, Michigan 49401, United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden. Electronic address: stenmark@dbb.su.se.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Seoul 08826, Republic of Korea.,Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States.,d Department of Cell Biology , Harvard Medical School , Boston , MA , USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801 and.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA. Electronic address: lamb@ku.edu.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico.,Integrated Program in Neuroscience, McGill University, Montréal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,the Bio-based Materials Chemistry Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.,the Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260; acohen@slac.stanford.edu guc9@pitt.edu.,Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.,Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy.,Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK; Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan.,Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy.,Departments of Biochemistry and Molecular Genetics, MaRS Centre, West Tower, Floor 16, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada. Electronic address: derek.bowie@mcgill.ca.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wenty@im.ac.cn.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. takuhiro.ito@riken.jp.,Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.,Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan. Electronic address: sue@nodai.ac.jp.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,b Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.,Department of Integrative Oncology , BC Cancer Research Centre , V5Z 1L3 Vancouver Vancouver , British Columbia , Canada.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA.,University of Florence , NEUROFARBA Dept., Sezione di Scienze Farmaceutiche , Via Ugo Schiff 6 , 50019 Sesto Fiorentino ( Florence ), Italy.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.,c Collaborative Innovation Center of Chemistry for Life Sciences , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai , China.,Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy.,Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15260.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and yufeng@sinap.ac.cn.,From the Department of Biochemistry, s-nair@life.illinois.edu.,Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States.,From the Bioconversion Group and inoue-h@aist.go.jp.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.,Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Biochemistry and Molecular Biology, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden. Electronic address: gunnar@dbb.su.se.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia. mhinds@unimelb.edu.au.,From the Bioconversion Group and.,the University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. m.kvansakul@latrobe.edu.au.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.,Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States.,Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao Cancer Institute and School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Institute for Genomic Biology, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada. sli@uwo.ca.,The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; acohen@slac.stanford.edu guc9@pitt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetyl-alpha-D-glucosaminyl L-malate synthase
A, B
379Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: bshA (jojH, ypjH)
EC: 2.4.1.-
Find proteins for P42982 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42982
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
U5P
Query on U5P

Download SDF File 
Download CCD File 
B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
GMT
Query on GMT

Download SDF File 
Download CCD File 
A, B
(2S)-2-{[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid
C12 H19 N O10
COBMRTSHZAUOCY-BVKYVCSXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.660α = 90.00
b = 164.627β = 90.00
c = 97.729γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
Cootmodel building
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32GM093507
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM030910

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.2: 2019-05-01
    Type: Data collection, Database references