3P20

Crystal structure of vanadate bound subunit A of the A1AO ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase.

Manimekalai, M.S.Kumar, A.Jeyakanthan, J.Gruber, G.

(2011) J Mol Biol 408: 736-754

  • DOI: https://doi.org/10.1016/j.jmb.2011.03.010
  • Primary Citation of Related Structures:  
    3ND8, 3ND9, 3P20

  • PubMed Abstract: 

    Archaeal A-ATP synthases catalyze the formation of the energy currency ATP. The chemical mechanisms of ATP synthesis in A-ATP synthases are unknown. We have determined the crystal structure of a transition-like state of the vanadate-bound form of catalytic subunit A (A(Vi)) of the A-ATP synthase from Pyrococcus horikoshii OT3. Two orthovanadate molecules were observed in the A(Vi) structure, one of which interacts with the phosphate binding loop through residue S238. The second vanadate is positioned in the transient binding site, implicating for the first time the pathway for phosphate entry to the catalytic site. Moreover, since residues K240 and T241 are proposed to be essential for catalysis, the mutant structures of K240A and T241A were also determined. The results demonstrate the importance of these two residues for transition-state stabilization. The structures presented shed light on the diversity of catalytic mechanisms used by the biological motors A- and F-ATP synthases and eukaryotic V-ATPases.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain588Pyrococcus horikoshiiMutation(s): 1 
Gene Names: atpAPH1975
EC: 3.6.3.14
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
K [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
H [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
VO4
Query on VO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
I [auth A]
J [auth A]
L [auth A]
D [auth A],
F [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.55α = 90
b = 127.55β = 90
c = 104.064γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-04
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description