1NYW

The high resolution structures of RmlC from Streptoccus suis in complex with dTDP-D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High-Resolution Structures of RmlC from Streptococcus suis in Complex with Substrate Analogs Locate the Active Site of This Class of Enzyme

Dong, C.Major, L.L.Allen, A.Blankenfeldt, W.Maskell, D.Naismith, J.H.

(2003) Structure 11: 715-723

  • Primary Citation of Related Structures:  1NXM, 1NZC

  • PubMed Abstract: 
  • Nature achieves the epimerization of carbohydrates by a variety of chemical routes. One common route is that performed by the class of enzyme defined by dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from the rhamnose pathway. Earlier studies fa ...

    Nature achieves the epimerization of carbohydrates by a variety of chemical routes. One common route is that performed by the class of enzyme defined by dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from the rhamnose pathway. Earlier studies failed to identify the key residues in catalysis. We report the 1.3 A structure of RmlC from Streptococcus suis type 2 and its complexes with dTDP-D-glucose and dTDP-D-xylose. The streptococcal RmlC enzymes belong to a separate subgroup, sharing only 25% identity with RmlC from other bacteria, yet the S. suis enzyme has similar kinetic properties and structure to other RmlC enzymes. Structure, sequence alignment, and mutational analysis have now allowed reliable identification of the catalytic residues and their roles.


    Organizational Affiliation

    Centre for Biomolecular Science, The University, St. Andrews KY16 9ST, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
A, B
197Streptococcus suisGene Names: rmlC
EC: 5.1.3.13
Find proteins for Q8GIQ0 (Streptococcus suis)
Go to UniProtKB:  Q8GIQ0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAU
Query on DAU

Download SDF File 
Download CCD File 
A, B
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
C16 H26 N2 O16 P2
YSYKRGRSMLTJNL-URARBOGNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.586α = 90.00
b = 47.895β = 99.02
c = 72.417γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
SOLVEphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-23
    Type: Atomic model, Refinement description