3MZI

Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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This is version 1.1 of the entry. See complete history


Literature

Mutational and Structural Studies of the PixD BLUF Output Signal That Affects Light-Regulated Interactions with PixE.

Yuan, H.Dragnea, V.Wu, Q.Gardner, K.H.Bauer, C.E.

(2011) Biochemistry 50: 6365-6375

  • DOI: https://doi.org/10.1021/bi200701d
  • Primary Citation of Related Structures:  
    3MZI

  • PubMed Abstract: 

    PixD (Slr1694) is a BLUF (blue-light-using FAD) photoreceptor used by the cyanobacterium Synechocystis sp. PCC6803 to control phototaxis toward blue light. In this study, we probe the involvement of a conserved Tyr8-Gln50-Met93 triad in promoting an output signal upon blue light excitation of the bound flavin. Analysis of acrylamide quenching of Trp91 fluorescence shows that the side chain of this residue remains partially solvent exposed in both the lit and dark states. Mutational analysis demonstrates that substitution mutations at Tyr8 and Gln50 result in the loss of the photocycle while a mutation of Met93 does not appreciably disturb the formation of the light-excited state and only minimally accelerates its decay from 5.7 to 4.5 s. However, mutations of Tyr8, Gln50, and Met93 disrupt the ability of PixD dimers to interact with PixE to form a higher-order PixD(10)-PixE(5) complex, which is indicative of a lit conformational state. Solution nuclear magnetic resonance spectroscopy and X-ray crystallographic analyses confirm that a Tyr8 to Phe mutation is locked in a pseudo-light-excited state revealing flexible areas in PixD that likely constitute part of an output signal upon light excitation of wild-type PixD.


  • Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Activator of photopigment and puc expression
A, B, C, D, E
A, B, C, D, E, F
150Synechocystis sp. PCC 6803Mutation(s): 1 
Gene Names: slr1694
UniProt
Find proteins for P74295 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P74295 
Go to UniProtKB:  P74295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74295
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.85α = 90
b = 119.48β = 102.89
c = 93.26γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description