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: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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
  • Primary Citation of Related Structures:  
    3TIF

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized ABC transporter ATP-binding protein MJ0796AB235Methanocaldococcus jannaschii DSM 2661Mutation(s): 3 
Gene Names: MJ0796
Find proteins for Q58206 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58206 
Go to UniProtKB:  Q58206
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

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

Download CCD File 
A, B
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-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: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.649α = 90
b = 106.347β = 90
c = 117.232γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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
    Changes: Data collection