6GYX

Crystal structure of DacA from Staphylococcus aureus in complex with ApCpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.

Tosi, T.Hoshiga, F.Millership, C.Singh, R.Eldrid, C.Patin, D.Mengin-Lecreulx, D.Thalassinos, K.Freemont, P.Grundling, A.

(2019) PLoS Pathog. 15: e1007537-e1007537

  • DOI: 10.1371/journal.ppat.1007537
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus ...

    c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus aureus, c-di-AMP is produced by the membrane-anchored DacA enzyme. Inactivation of this enzyme leads to a growth arrest under standard laboratory growth conditions and a re-sensitization of methicillin-resistant S. aureus (MRSA) strains to ß-lactam antibiotics. The gene coding for DacA is part of the conserved three-gene dacA/ybbR/glmM operon that also encodes the proposed DacA regulator YbbR and the essential phosphoglucosamine mutase GlmM, which is required for the production of glucosamine-1-phosphate, an early intermediate of peptidoglycan synthesis. These three proteins are thought to form a complex in vivo and, in this manner, help to fine-tune the cellular c-di-AMP levels. To further characterize this important regulatory complex, we conducted a comprehensive structural and functional analysis of the S. aureus DacA and GlmM enzymes by determining the structures of the S. aureus GlmM enzyme and the catalytic domain of DacA. Both proteins were found to be dimers in solution as well as in the crystal structures. Further site-directed mutagenesis, structural and enzymatic studies showed that multiple DacA dimers need to interact for enzymatic activity. We also show that DacA and GlmM form a stable complex in vitro and that S. aureus GlmM, but not Escherichia coli or Pseudomonas aeruginosa GlmM, acts as a strong inhibitor of DacA function without the requirement of any additional cellular factor. Based on Small Angle X-ray Scattering (SAXS) data, a model of the complex revealed that GlmM likely inhibits DacA by masking the active site of the cyclase and preventing higher oligomer formation. Together these results provide an important mechanistic insight into how c-di-AMP production can be regulated in the cell.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA.,School of Biochemistry, Devi Ahilya University, Indore, India.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. emarcos82@gmail.com.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan. chinyuchen@cc.ncu.edu.tw.,Cyrus Biotechnology, Seattle, WA, USA.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and William.Royer@umassmed.edu.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: jtzheng@sjtu.edu.cn.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and.,the Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California, Irvine , Irvine , California 92697-3900 , United States.,Department of Biochemistry, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, Vandoeuvre-les-Nancy Cedex, France.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105 charles.rock@stjude.org.,School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,From the Departments of Structural Biology and.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.,Institute of Biochemistry, Graz University of Technology, Graz, Austria.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diadenylate cyclase
B, A
175N/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
MN
Query on MN

Download SDF File 
Download CCD File 
B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
APC
Query on APC

Download SDF File 
Download CCD File 
A, B
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.092α = 90.00
b = 80.424β = 90.00
c = 96.195γ = 90.00
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references