3MFY

Structural characterization of the subunit A mutant F236A of the A-ATP synthase from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding.

Kumar, A.Manimekalai, M.S.Balakrishna, A.M.Priya, R.Biukovic, G.Jeyakanthan, J.Gruber, G.

(2010) J.Mol.Biol. 401: 892-905

  • DOI: 10.1016/j.jmb.2010.06.070
  • Primary Citation of Related Structures:  
  • Also Cited By: 3QJY, 3QIA, 3QG1, 3P20

  • PubMed Abstract: 
  • The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A ...

    The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3. Both the structures show unique, altered conformations for the P-loop. Comparison with the previously solved wild type and P-loop mutant S238A structures of subunit A showed that the P-loop conformation for these two novel mutants occupy intermediate positions, with the wild type fully arched and the well-relaxed S238A mutant structures taking the extreme positions. Even though the deviation is similar for both mutants, the curvature of the P-loop faces the opposite direction. Deviations in the GER-loop, lying above the P-loop, are similar for both mutants, but in F236A, it moves towards the P-loop by around 2 A. The curvature of the loop region V392-V410, located directly behind the P-loop, moves close by 3.6 A towards the P-loop in the F236A structure and away by 2.5 A in the P235A structure. Two major deviations were observed in the P235A mutant, which are not identified in any of the subunit A structures analyzed so far, one being a wide movement of the N-terminal loop region (R90-P110) making a rotation of 80 degrees and the other being rigid-body rotation of the C-terminal helices from Q520-A588 by around 4 degrees upwards. Taken together, the data presented demonstrate the concerted effects of the critical residues P235A, F236, and S238 in the unique P-loop conformation of the A-ATP synthases.


    Related Citations: 
    • Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.
      Maegawa, Y.,Morita, H.,Iyaguchi, D.,Yao, M.,Watanabe, N.,Tanaka, I.
      (2006) Acta Crystallogr.,Sect.D 62: 483
    • Nucleotide Binding States of Subunit A of the A-ATP Synthase and the Implication of P-Loop Switch in Evolution.
      Kumar, A.,Manimekalai, M.S.S.,Balakrishna, A.M.,Jeyakanthan, J.,Gerhard, G.
      (2009) J.Mol.Biol. --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase alpha chain
A
588Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 2 
Gene Names: atpA
EC: 7.1.2.2
Find proteins for O57728 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O57728
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.535α = 90.00
b = 127.535β = 90.00
c = 106.785γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-23
    Type: Refinement description, Source and taxonomy