5X09 | pdb_00005x09

Crystal structure of subunit A mutant P235A/S238C of the A-ATP synthase from pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.272 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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Literature

Crystallographic and enzymatic insights into the mechanisms of Mg-ADP inhibition in the A1 complex of the A1AO ATP synthase

Singh, D.Gruber, G.

(2018) J Struct Biol 201: 26-35

  • DOI: https://doi.org/10.1016/j.jsb.2017.10.008
  • Primary Citation Related Structures: 
    5X09

  • PubMed Abstract: 

    F-ATP synthases are described to have mechanisms which regulate the unnecessary depletion of ATP pool during an energy limited state of the cell. Mg-ADP inhibition is one of the regulatory features where Mg-ADP gets entrapped in the catalytic site, preventing the binding of ATP and further inhibiting ATP hydrolysis. Knowledge about the existence and regulation of the related archaeal-type A 1 A O ATP synthases (A 3 B 3 CDE 2 FG 2 ac) is limited. We demonstrate MgADP inhibition of the enzymatically active A 3 B 3 D- and A 3 B 3 DF complexes of Methanosarcina mazei Gö1 A-ATP synthase and reveal the importance of the amino acids P235 and S238 inside the P-loop (GPFGSGKTV) of the catalytic A subunit. Substituting these two residues by the respective P-loop residues alanine and cysteine (GAFGCGKTV) of the related eukaryotic V-ATPase increases significantly the ATPase activity of the enzyme variant and abolishes MgADP inhibition. The atomic structure of the P235A, S238C double mutant of subunit A of the Pyrococcus horikoshii OT3 A-ATP synthase provides details of how these critical residues affect nucleotide-binding and ATP hydrolysis in this molecular engine. The qualitative data are confirmed by quantitative results derived from fluorescence correlation spectroscopy experiments.


  • Organizational Affiliation
    • Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.

Macromolecule Content 

  • Total Structure Weight: 60.81 kDa 
  • Atom Count: 4,342 
  • Modeled Residue Count: 530 
  • Deposited Residue Count: 538 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain,V-type ATP synthase alpha chain538Pyrococcus horikoshii OT3Mutation(s): 3 
Gene Names: atpAPH1975
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for O57728 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57728 
Go to UniProtKB:  O57728
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57728
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.272 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.467α = 90
b = 127.467β = 90
c = 105.349γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of educationSingaporeMOE2011-T2-2-156; ARC 18/12

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description