3TIF

Dimeric structure of a post-hydrolysis state of the ATP-binding cassette MJ0796 bound to ADP and Pi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7995 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kinetics of the association/dissociation cycle of an ATP-binding cassette nucleotide-binding domain.

Zoghbi, M.E.Fuson, K.L.Sutton, R.B.Altenberg, G.A.

(2012) J.Biol.Chem. 287: 4157-4164

  • DOI: 10.1074/jbc.M111.318378

  • PubMed Abstract: 
  • Most ATP binding cassette (ABC) proteins are pumps that transport substrates across biological membranes using the energy of ATP hydrolysis. Functional ABC proteins have two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP, but the molec ...

    Most ATP binding cassette (ABC) proteins are pumps that transport substrates across biological membranes using the energy of ATP hydrolysis. Functional ABC proteins have two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP, but the molecular mechanism of nucleotide hydrolysis is unresolved. This is due in part to the limited kinetic information on NBD association and dissociation. Here, we show dimerization of a catalytically active NBD and follow in real time the association and dissociation of NBDs from the changes in fluorescence emission of a tryptophan strategically located at the center of the dimer interface. Spectroscopic and structural studies demonstrated that the tryptophan can be used as dimerization probe, and we showed that under hydrolysis conditions (millimolar MgATP), not only the dimer dissociation rate increases, but also the dimerization rate. Neither dimer formation or dissociation are clearly favored, and the end result is a dynamic equilibrium where the concentrations of monomer and dimer are very similar. We proposed that based on their variable rates of hydrolysis, the rate-limiting step of the hydrolysis cycle may differ among full-length ABC proteins.


    Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Texas Tech Health Sciences Center, Lubbock, Texas 79430-6551, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized ABC transporter ATP-binding protein MJ0796
A, B
235Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 3 
Find proteins for Q58206 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58206
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PI
Query on PI

Download SDF File 
Download CCD File 
A, B
HYDROGENPHOSPHATE ION
H O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd: 4200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7995 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.649α = 90.00
b = 106.347β = 90.00
c = 117.232γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
ADSCdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-08-20 
  • Released Date: 2012-03-21 
  • Deposition Author(s): Sutton, R.B.

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Data collection