4HH1 | pdb_00004hh1

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/nsmb.2597
  • Primary Citation Related Structures: 
    4HH0, 4HH1, 4HH2, 4HH3

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 88.66 kDa 
  • Atom Count: 5,862 
  • Modeled Residue Count: 765 
  • Deposited Residue Count: 812 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AppA protein
A, B
406Cereibacter sphaeroidesMutation(s): 1 
Gene Names: appA
UniProt
Find proteins for Q53119 (Cereibacter sphaeroides)
Explore Q53119 
Go to UniProtKB:  Q53119
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53119
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.53α = 90
b = 70.53β = 90
c = 383.81γ = 120
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-07-17
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations