3M9W

Open ligand-free crystal structure of xylose binding protein from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed

Sooriyaarachchi, S.Ubhayasekera, W.Park, C.Mowbray, S.L.

(2010) J.Mol.Biol. 402: 657-668

  • DOI: 10.1016/j.jmb.2010.07.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ATP binding cassette transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing cognate ligand and directing it to the approp ...

    ATP binding cassette transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing cognate ligand and directing it to the appropriate membrane permease. Here we report the X-ray structures of D-xylose binding protein from Escherichia coli in ligand-free open form, ligand-bound open form, and ligand-bound closed form at 2.15 Å, 2.2 Å, and 2.2 Å resolutions, respectively. The ligand-bound open form is the first such structure to be reported at high resolution; the combination of the three different forms from the same protein furthermore gives unprecedented details concerning the conformational changes involved in binding protein function. As is typical of the structural family, the protein has two similar globular domains, which are connected by a three-stranded hinge region. The open liganded structure shows that xylose binds first to the C-terminal domain, with only very small conformational changes resulting. After a 34° closing motion, additional interactions are formed with the N-terminal domain; changes in this domain are larger and serve to make the structure more ordered near the ligand. An analysis of the interactions suggests why xylose is the preferred ligand. Furthermore, a comparison with the most closely related proteins in the structural family shows that the conformational changes are distinct in each type of binding protein, which may have implications for how the individual proteins act in concert with their respective membrane permeases.


    Organizational Affiliation

    Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-xylose-binding periplasmic protein
A
313Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: xylF (xylT)
Find proteins for P37387 (Escherichia coli (strain K12))
Go to UniProtKB:  P37387
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.663α = 90.00
b = 72.188β = 100.48
c = 66.322γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
MxCuBEdata collection
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-05
    Type: Database references