3RYK

1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC).

Shornikov, A.Tran, H.Macias, J.Halavaty, A.S.Minasov, G.Anderson, W.F.Kuhn, M.L.

(2017) Acta Crystallogr F Struct Biol Commun 73: 664-671

  • DOI: 10.1107/S2053230X17015849
  • Primary Citation of Related Structures:  
    3RYK

  • PubMed Abstract: 
  • The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to ...

    The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, San Francisco State University, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dTDP-4-dehydrorhamnose 3,5-epimeraseAB205Bacillus anthracis str. AmesMutation(s): 0 
Gene Names: BAS1136BA_1229GBAA_1229rfbC
EC: 5.1.3.13
Find proteins for A0A1S0QLH9 (Bacillus anthracis)
Explore A0A1S0QLH9 
Go to UniProtKB:  A0A1S0QLH9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download CCD File 
B
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
POP
Query on POP

Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: P 3
  • Diffraction Data DOI: 10.18430/M33RYK Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.652α = 90
b = 86.652β = 90
c = 45.101γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-06-21
    Changes: Advisory, Atomic model, Derived calculations
  • Version 2.1: 2017-11-08
    Changes: Refinement description
  • Version 2.2: 2017-12-13
    Changes: Database references
  • Version 2.3: 2018-04-18
    Changes: Data collection, Database references