8QFF

Cryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC with ATP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Light-induced Trp in /Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC.

Chretien, A.Nagel, M.F.Botha, S.de Wijn, R.Brings, L.Dorner, K.Han, H.Koliyadu, J.C.P.Letrun, R.Round, A.Sato, T.Schmidt, C.Secareanu, R.C.von Stetten, D.Vakili, M.Wrona, A.Bean, R.Mancuso, A.Schulz, J.Pearson, A.R.Kottke, T.Lorenzen, K.Schubert, R.

(2024) J Mol Biol 436: 168439-168439

  • DOI: https://doi.org/10.1016/j.jmb.2024.168439
  • Primary Citation of Related Structures:  
    8QFE, 8QFF, 8QFG, 8QFH, 8QFI, 8QFJ

  • PubMed Abstract: 

    The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trp in /Met out transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.


  • Organizational Affiliation

    European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Family 3 adenylate cyclase350Oscillatoria acuminata PCC 6304Mutation(s): 0 
Gene Names: Oscil6304_3613
UniProt
Find proteins for K9TLZ5 (Oscillatoria acuminata PCC 6304)
Explore K9TLZ5 
Go to UniProtKB:  K9TLZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9TLZ5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.455α = 90
b = 146.435β = 90
c = 104.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Database references