2DRI

PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 30206-30211

  • Primary Citation of Related Structures:  1DRJ, 1DRK

  • PubMed Abstract: 
  • A number of mutations at Gly134 of the periplasmic ribose-binding protein of Escherichia coli were examined by a combined biochemical and structural approach. Different mutations gave rise to different patterns of effects on the chemotaxis and transp ...

    A number of mutations at Gly134 of the periplasmic ribose-binding protein of Escherichia coli were examined by a combined biochemical and structural approach. Different mutations gave rise to different patterns of effects on the chemotaxis and transport functions. The smallest residue (alanine) had the least effect on transport, whereas large hydrophobic residues had the smallest effect on chemotaxis. Comparison of the x-ray crystal structure of the G134R mutant protein (2.5-A resolution) to that of the wild type (1.6-A resolution) showed that the basic structure of the protein was unaltered. The loss of chemotaxis and transport functions in this and similar mutant proteins must therefore be caused by relatively simple surface effects, which include a change in local main chain conformation. The loss of chemotaxis and transport functions resulting from the introduction of an alanine residue at position 134 was suppressed by an additional isoleucine to threonine mutation at residue 132. An x-ray structure of the I132T/G134A double mutant protein (2.2-A resolution) showed that the changes in local structure were accompanied by a diffuse pattern of structural changes in the surrounding region, implying that the suppression derives from a combination of sources.


    Related Citations: 
    • Preliminary X-Ray Data for the Periplasmic Ribose Receptor from Escherichia Coli
      Mahendroo, M.,Cole, L.B.,Mowbray, S.L.
      (1990) J.Mol.Biol. 211: 689
    • Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations which Affect Chemotaxis and Transport
      Binnie, R.A.,Zhang, H.,Mowbray, S.,Hermodson, M.A.
      (1992) Protein Sci. 1: 1642
    • 1.7 Angstroms X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli
      Mowbray, S.L.,Cole, L.B.
      (1992) J.Mol.Biol. 225: 155


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-RIBOSE-BINDING PROTEIN
A
271Escherichia coli (strain K12)Gene Names: rbsB (prlB, rbsP)
Find proteins for P02925 (Escherichia coli (strain K12))
Go to UniProtKB:  P02925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIP
Query on RIP

Download SDF File 
Download CCD File 
A
RIBOSE(PYRANOSE FORM)
C5 H10 O5
SRBFZHDQGSBBOR-TXICZTDVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RIPKd: 130 nM BINDINGMOAD
RIPKd: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.920α = 90.00
b = 88.990β = 90.00
c = 40.270γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-01-26
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other