6PU2

Dark, Mutant H275T , 100K, PCM Myxobacterial Phytochrome, P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.

Sanchez, J.C.Carrillo, M.Pandey, S.Noda, M.Aldama, L.Feliz, D.Claesson, E.Wahlgren, W.Y.Tracy, G.Duong, P.Nugent, A.C.Field, A.Srajer, V.Kupitz, C.Iwata, S.Nango, E.Tanaka, R.Tanaka, T.Fangjia, L.Tono, K.Owada, S.Westenhoff, S.Schmidt, M.Stojkovic, E.A.

(2019) Struct Dyn. 6: 054701-054701

  • DOI: 10.1063/1.5120527
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red ligh ...

    Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca ( Sa BphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.


    Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.,The University of Chicago, Center for Advanced Radiation Sources, 9700 South Cass Ave., Bldg 434B, Argonne, Illinois 60439, USA.,Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, Illinois 60625, USA.,Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, Wisconsin 53211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoreceptor-histidine kinase BphP
A, B
481Stigmatella aurantiaca (strain DW4/3-1)Mutation(s): 1 
EC: 2.7.13.3
Find proteins for Q09E27 (Stigmatella aurantiaca (strain DW4/3-1))
Go to UniProtKB:  Q09E27
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EL5
Query on EL5

Download SDF File 
Download CCD File 
A, B
Biliverdin
C33 H36 N4 O6
SNHIGJASYQUMKZ-IDFYGOSVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.405α = 90.00
b = 81.790β = 107.00
c = 83.493γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United States--

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release