5IRP

Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.

Bernardo-Garcia, N.Sanchez-Murcia, P.A.Espaillat, A.Martinez-Caballero, S.Cava, F.Hermoso, J.A.Gago, F.

(2019) Org.Biomol.Chem. 17: 4350-4358

  • DOI: 10.1039/c9ob00223e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound ...

    Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Genome Sciences, University of Washington, Seattle, United States.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. stefano.ciurli@unibo.it.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina, 27710, USA. awilliam@pasteur.fr.,Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wfeng@ibp.ac.cn.,Engineering Research Center for the Development and Application of Ethnic Medicine and TCM, Ministry of Education, Guizhou Medical University, Guiyang, China.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. yingxuxu@shsmu.edu.cn.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China.,Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: ckerfeld@lbl.gov.,JSC Spronk, Vilnius, Lithuania.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA. zaw@uga.edu.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. jysuh@snu.ac.kr.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada. burrowl@mcmaster.ca.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA.,School of Life Sciences and Technology, Tongji University, Shanghai, China.,Broad Institute of MIT and Harvard, Cambridge, MA, United States of America.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom.,Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.,Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.,Department of Biochemistry, University of Washington, Seattle, United States.,Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.,Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui 230027, China.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America.,State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Howard Hughes Medical Institute, Departments of Physiology and Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Drug Discovery Group Cancer Research UK Manchester Institute, Manchester, UK.,the Departments of Life Sciences and.,Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil. kleber.franchini@lnbio.cnpem.br.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,D. E. Shaw Research, New York, NY, USA.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.,The Hamburg Centre for Ultrafast Imaging, Germany.,Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.,Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain. xjuan@iqfr.csic.es.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,Department of Microbiology, University of Washington, Seattle, United States.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,Shanghai Institute of Precision Medicine, Shanghai 200125, China.,Program in Molecular Structure & Function, The Hospital for Sick Children, Toronto, ON, Canada. howell@sickkids.ca.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. juliana.oliveira@lnbio.cnpem.br.,Chemistry and Biochemistry, University of Arizona, 1041 East Lowell Drive, Biosciences West, Tucson, AZ 85281, USA.,European XFEL GmbH, Schenefeld, Germany.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. chengq@shsmu.edu.cn.,Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.,Department of Biochemistry, Western University, London, ON, Canada.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.,National Center for Protein Science Shanghai, Shanghai 201203, China liqiong@ustc.edu.cn nli@sibcb.ac.cn.,Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia.,Department of Biological Chemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, MD9, Singapore.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: penchit@biotec.or.th.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, wipa@sut.ac.th.,Biomedical Sciences, Defence Science and Technology Laboratory Porton Down, SP4 0JQ Salisbury, United Kingdom.,From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. kleber.franchini@lnbio.cnpem.br.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.,Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA. cnathan@med.cornell.edu sacchett@tamu.edu.,Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China.,Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China. chaijj@tsinghua.edu.cn jmzhou@genetics.ac.cn hongweiwang@tsinghua.edu.cn.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 28 Rue du Dr. Roux, 75015, Paris, France. awilliam@pasteur.fr.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602; zaw@uga.edu moremen@uga.edu.,Abteilung molelukare Biowissensschaften, Molekulare Zellbiologie der Pflanzen, Goethe Universität, Frankfurt am Main, Germany.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina, 27710, USA.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, 980-8577 Sendai, Japan.,Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA. mmaroney@chem.umass.edu.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA. David.Thanassi@stonybrook.edu.,Mechanobiology Institute, National University of Singapore, Singapore.,Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Medicinal Chemistry, Department of Internal Medicine, Comprehensive Cancer Center, and Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A. seongminlee@austin.utexas.edu.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.,Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Department of Chemistry, University of Georgia, Athens, GA, USA.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502 Kyoto, Japan; miki@kuchem.kyoto-u.ac.jp.,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy. stefano.ciurli@unibo.it.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8510 Kyoto, Japan.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Sorbonne Université, Collège doctoral, 75005, Paris, France.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia. Electronic address: r.mcgeary@uq.edu.au.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Institute of Biocomputation and Physics of Complex Systems (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Spain, Department of Biochemistry and Molecular and Cellular Biology, Universidad de Zaragoza, Fundacion ARAID, Gobierno de Aragon, Spain, Aragon Health Research Institute (IIS Aragon), Universidad de Zaragoza, Zaragoza, Spain.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K. jworrall@essex.ac.uk.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K. c.dong@uea.ac.uk.,Department of Medicine, University of Washington, Seattle, United States.,Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France.,Structural Biology Research Center, VIB, Brussels, Belgium.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.,the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. howell@sickkids.ca.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan.,Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan. jysuh@snu.ac.kr.,Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.,Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, 102-0076 Tokyo, Japan.,Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, 02792, Korea.,National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address: ubolsree@biotec.or.th.,Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Science Division, Mahidol University International College, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.,Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil.,From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.,Dropbox, New York, NY, USA.,Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France.,Bioss Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand.,Medicinal Bioinformatics Center, Shanghai JiaoTong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.,CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France. jacqueline.cherfils@ens-paris-saclay.fr.,Basic Clinical Research Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.,the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alanine racemase 2
A, B
394Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: alr2 (yncD)
EC: 5.1.1.1
Find proteins for P94494 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94494
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
UAH
Query on UAH

Download SDF File 
Download CCD File 
A, B
(5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate
4'-deformyl pyidoxal phosphote
C7 H10 N O5 P
CKIPHKBHPIDPOG-UHFFFAOYSA-N
 Ligand Interaction
CO2
Query on CO2

Download SDF File 
Download CCD File 
B
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.154 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.888α = 90.00
b = 72.888β = 90.00
c = 332.833γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 2.0: 2019-04-24
    Type: Atomic model, Data collection, Database references
  • Version 2.1: 2019-05-08
    Type: Advisory, Data collection, Database references