1URP

D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Multiple open forms of ribose-binding protein trace the path of its conformational change.

Bjorkman, A.J.Mowbray, S.L.

(1998) J.Mol.Biol. 279: 651-664

  • DOI: 10.1006/jmbi.1998.1785
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conformational changes are necessary for the function of bacterial periplasmic receptors in chemotaxis and transport. Such changes allow entry and exit of ligand, and enable the correct interaction of the ligand-bound proteins with the membrane compo ...

    Conformational changes are necessary for the function of bacterial periplasmic receptors in chemotaxis and transport. Such changes allow entry and exit of ligand, and enable the correct interaction of the ligand-bound proteins with the membrane components of each system. Three open, ligand-free forms of the Escherichia coli ribose-binding protein were observed here by X-ray crystallographic studies. They are opened by 43 degrees, 50 degrees and 64 degrees with respect to the ligand-bound protein reported previously. The three open forms are not distinct, but show a clear relationship to each other. All are the product of a similar opening motion, and are stabilized by a new, almost identical packing interface between the domains. The changes are generated by similar bond rotations, although some differences in the three hinge segments are needed to accommodate the various structural scenarios. Some local repacking also occurs as interdomain contacts are lost. The least open (43 degrees) form is probably the dominant one in solution under normal conditions, although a mixture of species seems likely. The open and closed forms have distinct surfaces in the regions known to be important in chemotaxis and transport, which will differentiate their interactions with the membrane components. It seems certain that the conformational path that links the forms described here is that followed during ligand retrieval, and in ligand release into the membrane-bound permease system.


    Related Citations: 
    • 1.7 A X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli
      Mowbray, S.L.,Cole, L.B.
      (1992) J.Mol.Biol. 225: 155
    • Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations that Affect Chemotaxis and Transport
      Binnie, R.A.,Zhang, H.,Mowbray, S.,Hermodson, M.A.
      (1992) Protein Sci. 1: 1642
    • Identical Mutations at Corresponding Positions in Two Homologous Proteins with Nonidentical Effects
      Bjorkman, A.J.,Binnie, R.A.,Cole, L.B.,Zhang, H.,Hermodson, M.A.,Mowbray, S.L.
      (1994) J.Biol.Chem. 269: 11196
    • Probing Protein-Protein Interactions. The Ribose-Binding Protein in Bacterial Transport and Chemotaxis
      Bjorkman, A.J.,Binnie, R.A.,Zhang, H.,Cole, L.B.,Hermodson, M.A.,Mowbray, S.L.
      (1994) J.Biol.Chem. 269: 30206


    Organizational Affiliation

    Department of Molecular Biology, Swedish Agricultural University, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-RIBOSE-BINDING PROTEIN
A, B, C, D
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rbsB (prlB, rbsP)
Find proteins for P02925 (Escherichia coli (strain K12))
Go to UniProtKB:  P02925
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.099α = 90.00
b = 120.954β = 90.05
c = 64.131γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance