4CBK

The c-ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic cell physiology


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The C-Ring Ion-Binding Site of the ATP Synthase from Bacillus Pseudofirmus of4 is Adapted to Alkaliphilic Lifestyle.

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

(2014) Mol Microbiol 92: 973

  • DOI: 10.1111/mmi.12605
  • Primary Citation of Related Structures:  
    4CBK, 4CBJ

  • PubMed Abstract: 
  • In the c-ring rotor of ATP synthases ions are shuttled across the membrane during ATP synthesis by a unique rotary mechanism. We investigated characteristics of the c-ring from the alkaliphile Bacillus pseudofirmus OF4 with respect to evolutionary adaptations to operate with protons at high environmental pH ...

    In the c-ring rotor of ATP synthases ions are shuttled across the membrane during ATP synthesis by a unique rotary mechanism. We investigated characteristics of the c-ring from the alkaliphile Bacillus pseudofirmus OF4 with respect to evolutionary adaptations to operate with protons at high environmental pH. The X-ray structures of the wild-type c13 ring at pH 9.0 and a 'neutralophile-like' mutant (P51A) at pH 4.4, at 2.4 and 2.8 Å resolution, respectively, reveal a dependency of the conformation and protonation state of the proton-binding glutamate (E(54) ) on environmental hydrophobicity. Faster labelling kinetics with the inhibitor dicyclohexylcarbodiimide (DCCD) demonstrate a greater flexibility of E(54) in the mutant due to reduced water occupancy within the H(+) binding site. A second 'neutralophile-like' mutant (V21N) shows reduced growth at high pH, which is explained by restricted conformational freedom of the mutant's E(54) carboxylate. The study directly connects subtle structural adaptations of the c-ring ion binding site to in vivo effects of alkaliphile cell physiology.


    Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT C
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M
69Bacillus pseudofirmus OF4Mutation(s): 0 
Gene Names: atpEBpOF4_06875
Find proteins for P22483 (Alkalihalobacillus pseudofirmus (strain ATCC BAA-2126 / JCM 17055 / OF4))
Explore P22483 
Go to UniProtKB:  P22483
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
Q [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DPV
Query on DPV

Download Ideal Coordinates CCD File 
AA [auth G] , CA [auth H] , EA [auth I] , FA [auth J] , HA [auth K] , JA [auth L] , KA [auth M] , N [auth A] , 
AA [auth G],  CA [auth H],  EA [auth I],  FA [auth J],  HA [auth K],  JA [auth L],  KA [auth M],  N [auth A],  P [auth B],  S [auth C],  U [auth D],  W [auth E],  Y [auth F]
dodecyl 2-(trimethylammonio)ethyl phosphate
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth H] , DA [auth I] , GA [auth K] , IA [auth L] , O [auth B] , R [auth C] , T [auth D] , V [auth E] , 
BA [auth H],  DA [auth I],  GA [auth K],  IA [auth L],  O [auth B],  R [auth C],  T [auth D],  V [auth E],  X [auth F],  Z [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A , B , C , D , E , F , G , H , 
A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L,  M
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.79α = 90
b = 96.75β = 105.38
c = 118.33γ = 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: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references