Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 72443.65 
• Atom Count: 5082 
• Residue Count: 655 
• Unique protein chains: 1

1OGE

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

• DOI: 10.2210/pdb1OGE/pdb

• Classification: TRANSPORT
• Organism(s): Bacillus subtilis (strain 168)


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

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Experimental Data Snapshot

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

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

• PubMed: 12738765 
• DOI: 10.1074/jbc.M304523200
• Primary Citation of Related Structures:  
  1OGF, 1OGD, 1OGC


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD	A, B, C, D, E	131	Bacillus 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
RP5	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
CL	A, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 123.807	α = 90.00
b = 108.556	β = 128.72
c = 83.532	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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
• Version 1.3: 2019-05-22
  Type: Data collection, Other, Refinement description