1NYW | pdb_00001nyw

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

• PDB DOI: https://doi.org/10.2210/pdb1NYW/pdb

• Classification: ISOMERASE
• Organism(s): Streptococcus suis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-02-14 Released: 2003-06-24 
• Deposition Author(s): Dong, C., Major, L.L., Allen, A., Blankenfeldt, W., Maskell, D., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.217 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

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

• PubMed: 12791259 
• DOI: https://doi.org/10.1016/s0969-2126(03)00098-4
• Primary Citation Related Structures: 
  1NXM, 1NYW, 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 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.

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Organizational Affiliation: 
• Centre for Biomolecular Science, The University, St. Andrews KY16 9ST, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 46.11 kDa 
• Atom Count: 3,730 
• Modeled Residue Count: 389 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase	A, B	197	Streptococcus suis	Mutation(s): 0  Gene Names: rmlc EC: 5.1.3.13
UniProt
Find proteins for Q8GIQ0 (Streptococcus suis) Explore Q8GIQ0  Go to UniProtKB:  Q8GIQ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAU	C [auth A], D [auth B]	2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE C16 H26 N2 O16 P2 YSYKRGRSMLTJNL-URARBOGNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.217 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.586	α = 90
b = 47.895	β = 99.02
c = 72.417	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-24 
Deposition Author(s): Dong, C., Major, L.L., Allen, A., Blankenfeldt, W., Maskell, D., Naismith, J.H.

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-05-23
  Changes: Atomic model, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description