4CBK | pdb_00004cbk

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 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1111/mmi.12605
  • Primary Citation Related Structures: 
    4CBJ, 4CBK

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 96.15 kDa 
  • Atom Count: 6,790 
  • Modeled Residue Count: 897 
  • Deposited Residue Count: 897 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT C
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M
69Alkalihalophilus pseudofirmus OF4Mutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / 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
DPV

Query on DPV



Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth H]
EA [auth I]
FA [auth J]
HA [auth K]
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
NA

Query on NA



Download:Ideal Coordinates CCD File
BA [auth H]
DA [auth I]
GA [auth K]
IA [auth L]
O [auth B]
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, B, C, D, E
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 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
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

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary