4HH1

Dark-state structure of AppA wild-type without the Cys-rich region from Rb. sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.

Winkler, A.Heintz, U.Lindner, R.Reinstein, J.Shoeman, R.L.Schlichting, I.

(2013) Nat.Struct.Mol.Biol. 20: 859-867

  • DOI: 10.1038/nsmb.2597
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy sources, depending on environmental conditions including aerobic respiration or, in the absence of oxygen, photosynthesis. Photosynthetic genes are repressed at high ...

    The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy sources, depending on environmental conditions including aerobic respiration or, in the absence of oxygen, photosynthesis. Photosynthetic genes are repressed at high oxygen tension, but at intermediate levels their partial expression prepares the bacterium for using light energy. Illumination, however, enhances repression under semiaerobic conditions. Here, we describe molecular details of two proteins mediating oxygen and light control of photosynthesis-gene expression: the light-sensing antirepressor AppA and the transcriptional repressor PpsR. Our crystal structures of both proteins and their complex and hydrogen/deuterium-exchange data show that light activation of AppA-PpsR2 affects the PpsR effector region within the complex. DNA binding studies demonstrate the formation of a light-sensitive ternary AppA-PpsR-DNA complex. We discuss implications of these results for regulation by light and oxygen, highlighting new insights into blue light-mediated signal transduction.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany. andreas.winkler@mpimf-heidelberg.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AppA protein
A, B
406Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: appA
Find proteins for Q53119 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q53119
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 70.530α = 90.00
b = 70.530β = 90.00
c = 383.810γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
XSCALEdata scaling
PHENIXmodel building
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2013-07-17
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description