1OGE

The Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture

Kim, M.-S., Shin, J., Lee, W., Lee, H.-S., Oh, B.-H.

(2003) J.Biol.Chem. 278: 28173

  • DOI: 10.1074/jbc.M304523200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose functi ...

    RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.

    Organizational Affiliation: 

    Center for Biomolecular Recognition and Division of Molecular and Life Science, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
A, B, C, D, E
131Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rbsD
EC: 5.4.99.62
Find proteins for P36946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P36946
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RP5
Query on RP5
Download SDF File 
Download CCD File 
A, B, C, D, E
5-O-phosphono-beta-D-ribofuranose
[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
C5 H11 O8 P
KTVPXOYAKDPRHY-TXICZTDVSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.807α = 90.00
b = 108.556β = 128.72
c = 83.532γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2003-04-30 
  • Released Date: 2003-09-01 
  • Deposition Author(s): Kim, M.-S., Oh, B.-H.

Revision History 

  • Version 1.0: 2003-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance