2CK3

Azide inhibited bovine F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How Azide Inhibits ATP Hydrolysis by the F-Atpases.

Bowler, M.W.Montgomery, M.G.Leslie, A.G.Walker, J.E.

(2006) Proc.Natl.Acad.Sci.USA 103: 8646

  • DOI: 10.1073/pnas.0602915103

  • PubMed Abstract: 
  • In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding ca ...

    In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.


    Related Citations: 
    • Tructure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites Implications for the Mechanism of Rotary Catalysis
      Menz, R.I.,Walker, J.E.,Leslie, A.G.W.
      (2001) Cell 106: 331
    • The Structure of the Central Stalk in Bovine F1- ATPase at 2.4A Resolution
      Gibbons, C.,Montgomery, M.G.,Leslie, A.G.W.,Walker, J.E.
      (2000) Nat.Struct.Mol.Biol. 7: 1055
    • Reproducible Improvements in Order and Diffraction Limit of Crystals of Bovine Mitochondrial F(1)- ATPase by Controlled Dehydration.
      Bowler, M.W.,Montgomery, M.G.,Leslie, A.G.,Walker, J.E.
      (2006) Acta Crystallogr.,Sect.D 62: 991
    • ATP Synthesis by Rotary Catalysis (Nobel Lecture)
      Walker, J.E.
      (1998) Angew.Chem.Int.Ed.Engl. 37: 2308
    • The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride
      Kagawa, R.,Montgomery, M.G.,Braig, K.,Leslie, A.G.W.,Walker, J.E.
      (2004) Embo J. 23: 2734
    • Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
      Abrahams, J.P.,Leslie, A.G.W.,Lutter, R.,Walker, J.E.
      (1994) Nature 370: 621
    • Crystallization of F1-ATPase from Bovine Heart Mitochondria
      Lutter, R.,Abrahams, J.P.,Van Raaij, M.J.,Todd, R.J.,Lundqvist, T.,Buchanan, S.K.,Leslie, A.G.,Walker, J.E.
      (1993) J.Mol.Biol. 229: 787
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D.,Leslie, A.G.W.,Walker, J.E.
      (1999) Science 286: 1700


    Organizational Affiliation

    Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C
510Bos taurusGene Names: ATP5A1 (ATP5A2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P19483 (Bos taurus)
Go to Gene View: ATP5A1
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F
482Bos taurusGene Names: ATP5B
EC: 3.6.3.14
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P00829 (Bos taurus)
Go to Gene View: ATP5B
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G
272Bos taurusGene Names: ATP5C1 (ATP5C)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05631 (Bos taurus)
Go to Gene View: ATP5C1
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H
146Bos taurusGene Names: ATP5D
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05630 (Bos taurus)
Go to Gene View: ATP5D
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I
50Bos taurusGene Names: ATP5E
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05632 (Bos taurus)
Go to Gene View: ATP5E
Go to UniProtKB:  P05632
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
D
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 261.160α = 90.00
b = 105.220β = 90.00
c = 122.730γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Refinement description, Version format compliance
  • Version 1.2: 2014-01-22
    Type: Database references, Refinement description, Structure summary