4FPD

Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.243 

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This is version 1.1 of the entry. See complete history


Literature

Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway.

Wang, T.Sessions, A.O.Lunde, C.S.Rouhani, S.Glaeser, R.M.Duan, Y.Facciotti, M.T.

(2013) Structure 21: 290-297

  • DOI: 10.1016/j.str.2012.12.018
  • Primary Citation of Related Structures:  
    4FPD

  • PubMed Abstract: 
  • Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR ...

    Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR and 60 independent molecular dynamics simulations of bR photointermediates, we report that the deprotonation of D96, a key residue in proton transfer reactions, serves two roles that occur sequentially. First, D96 donates a proton to the Schiff base. Subsequently, the deprotonation of D96 serves to "unlatch" the cytoplasmic side. The latching function of D96 appears to be remarkably robust, functioning to open hydration channels in all photointermediate structures. These results suggest that the protonation state of D96 may be the critical biophysical cue controlling the opening and closing of the cytoplasmic half-channel in bR. We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality.


    Organizational Affiliation

    Genome Center and Department of Biomedical Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bacteriorhodopsin A262Halobacterium salinarum NRC-1Mutation(s): 3 
Gene Names: bopVNG_1467G
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, Viral, and Unusual Rhodopsins
Protein: 
Bacteriorhodopsin (BR); D96/F171C/F219L mutant
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.243 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.931α = 90
b = 60.931β = 90
c = 107.701γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Source and taxonomy, Structure summary