3I73

Structural characterization for the nucleotide binding ability of subunit A with ADP of the A1AO ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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.Balakrishna, A.M.Jeyakanthan, J.Gruber, G.

(2010) J.Mol.Biol. 396: 301-320

  • DOI: 10.1016/j.jmb.2009.11.046
  • Primary Citation of Related Structures:  
  • Also Cited By: 3SE0, 3SDZ, 3QJY, 3QIA, 3QG1, 3P20, 3ND9, 3ND8, 3MFY, 3M4Y

  • PubMed Abstract: 
  • The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have bee ...

    The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the A(E) form, the phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.


    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


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A
A
588Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 1 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd: 3230 nM BINDINGMOAD
ADPKd: 3230 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.472α = 90.00
b = 128.472β = 90.00
c = 104.991γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-11-13
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-01
    Type: Refinement description