2V93

EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 50 
  • Selection Criteria: PRE AND VDW ENERGIES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Open-to-Closed Transition in Apo Maltose-Binding Protein Observed by Paramagnetic NMR.

Tang, C.Schwieters, C.D.Clore, G.M.

(2007) Nature 449: 1078

  • DOI: 10.1038/nature06232

  • PubMed Abstract: 
  • Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usua ...

    Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.


    Organizational Affiliation

    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALTOSE-BINDING PERIPLASMIC PROTEIN
A
370Escherichia coli (strain K12)Mutations: C211S, C41D
Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MXT
Query on MXT

Download SDF File 
Download CCD File 
A
1-(1-HYDROXY-2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)PYRROLIDINE-2,5-DIONE
C13 H22 N2 O3
ZHMZILPINCAHPK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 50 
  • Selection Criteria: PRE AND VDW ENERGIES 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-08-21 
  • Released Date: 2007-11-06 
  • Deposition Author(s): Clore, G.M., Tang, C.

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance