6BAY

Stigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289H mutant, room temperature structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome.

Woitowich, N.C.Halavaty, A.S.Waltz, P.Kupitz, C.Valera, J.Tracy, G.Gallagher, K.D.Claesson, E.Nakane, T.Pandey, S.Nelson, G.Tanaka, R.Nango, E.Mizohata, E.Owada, S.Tono, K.Joti, Y.Nugent, A.C.Patel, H.Mapara, A.Hopkins, J.Duong, P.Bizhga, D.Kovaleva, S.E.St Peter, R.Hernandez, C.N.Ozarowski, W.B.Roy-Chowdhuri, S.Yang, J.H.Edlund, P.Takala, H.Ihalainen, J.Brayshaw, J.Norwood, T.Poudyal, I.Fromme, P.Spence, J.C.H.Moffat, K.Westenhoff, S.Schmidt, M.Stojkovic, E.A.

(2018) IUCrJ 5: 619-634

  • DOI: 10.1107/S2052252518010631
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states ...

    Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxo-bacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.


    Organizational Affiliation

    Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,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.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.,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.,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.,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.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,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.,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.,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 Structural Biology, and.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,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.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Department of Physics, Ohio State University, Columbus, OH 43210.,Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,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 Molecular Physiology and Biophysics.,Department of Biology, Technische Universität Darmstadt, D64287 Darmstadt, Germany.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, 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.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, 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.,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 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.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.,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 Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoreceptor-histidine kinase BphP
A, B, C
515Stigmatella aurantiaca (strain DW4/3-1)Mutation(s): 1 
Find proteins for Q097N3 (Stigmatella aurantiaca (strain DW4/3-1))
Go to UniProtKB:  Q097N3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLR
Query on BLR

Download SDF File 
Download CCD File 
A, B, C
3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
Bilirubin IX alpha
C33 H36 N4 O6
BPYKTIZUTYGOLE-IFADSCNNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.230α = 90.00
b = 84.230β = 90.00
c = 477.990γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesSTC-1231306
National Science Foundation (United States)United StatesBIO-MCB 1413360
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT34 GM105549-01 NU-STARS
National Institutes of Health/National Eye InstituteUnited StatesEY024363
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM095583
Academy of FinlandFinland296135
Academy of FinlandFinland285461

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection