1OGC | pdb_00001ogc

The Structure of Bacillus subtilis RbsD complexed with D-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.231 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1OGC

This is version 1.4 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 Biological Chem 278: 28173

  • DOI: https://doi.org/10.1074/jbc.M304523200
  • Primary Citation Related Structures: 
    1OGC, 1OGD, 1OGE, 1OGF

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 71.29 kDa 
  • Atom Count: 5,198 
  • Modeled Residue Count: 655 
  • Deposited Residue Count: 655 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
A, B, C, D, E
131Bacillus subtilisMutation(s): 0 
EC: 5.4.99.62
UniProt
Find proteins for P36946 (Bacillus subtilis (strain 168))
Explore P36946 
Go to UniProtKB:  P36946
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36946
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.231 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.654α = 90
b = 108.14β = 128.92
c = 83.357γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references