3ZO6

Crystal structure of Bacillus pseudofirmus OF4 mutant ATP synthase c12 ring.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4.

Preiss, L.Klyszejko, A.L.Hicks, D.B.Liu, J.Fackelmayer, O.J.Yildiz, O.Krulwich, T.A.Meier, T.

(2013) Proc Natl Acad Sci U S A 110: 7874-7879

  • DOI: https://doi.org/10.1073/pnas.1303333110
  • Primary Citation of Related Structures:  
    3ZO6

  • PubMed Abstract: 

    The c-rings of ATP synthases consist of individual c-subunits, all of which harbor a conserved motif of repetitive glycine residues (GxGxGxG) important for tight transmembrane α-helix packing. The c-ring stoichiometry determines the number of ions transferred during enzyme operation and has a direct impact on the ion-to-ATP ratio, a cornerstone parameter of cell bioenergetics. In the extreme alkaliphile Bacillus pseudofirmus OF4, the glycine motif is replaced by AxAxAxA. We performed a structural study on two mutants with alanine-to-glycine changes using atomic force microscopy and X-ray crystallography, and found that mutants form smaller c12 rings compared with the WT c13. The molar growth yields of B. pseudofirmus OF4 cells on malate further revealed that the c12 mutants have a considerably reduced capacity to grow on limiting malate at high pH. Our results demonstrate that the mutant ATP synthases with either c12 or c13 can support ATP synthesis, and also underscore the critical importance of an alanine motif with c13 ring stoichiometry for optimal growth at pH >10. The data indicate a direct connection between the precisely adapted ATP synthase c-ring stoichiometry and its ion-to-ATP ratio on cell physiology, and also demonstrate the bioenergetic challenges and evolutionary adaptation strategies of extremophiles.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c69Alkalihalophilus pseudofirmus OF4Mutation(s): 2 
Gene Names: atpEBpOF4_06875
Membrane Entity: Yes 
UniProt
Find proteins for P22483 (Alkalihalophilus pseudofirmus (strain ATCC BAA-2126 / JCM 17055 / OF4))
Explore P22483 
Go to UniProtKB:  P22483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22483
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
B
C
D
E
A,
B,
C,
D,
E,
F,
G [auth H],
H [auth I],
I [auth J],
J [auth K],
K [auth L],
L [auth M]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.22α = 90
b = 114.55β = 90
c = 137.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2013-05-22
    Changes: Database references, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description