3SC6

2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose reductase (RfbD).

Law, A.Stergioulis, A.Halavaty, A.S.Minasov, G.Anderson, W.F.Kuhn, M.L.

(2017) Acta Crystallogr F Struct Biol Commun 73: 644-650

  • DOI: 10.1107/S2053230X17015746

  • PubMed Abstract: 
  • Bacillus anthracis is the causative agent of the deadly disease Anthrax. Its use in bioterrorism and its ability to re-emerge have brought renewed interest in this organism. B. anthracis is a Gram-positive bacterium that adds L-rhamnose to its cell-w ...

    Bacillus anthracis is the causative agent of the deadly disease Anthrax. Its use in bioterrorism and its ability to re-emerge have brought renewed interest in this organism. B. anthracis is a Gram-positive bacterium that adds L-rhamnose to its cell-wall polysaccharides using the activated donor dTDP-β-L-rhamnose. The enzymes involved in the biosynthesis of the activated donor are absent in humans, which make them ideal targets for therapeutic development to combat pathogens. Here, the 2.65 Å resolution crystal structure of the fourth enzyme in the dTDP-β-L-rhamnose-biosynthetic pathway from B. anthracis, dTDP-4-dehydro-β-L-rhamnose reductase (RfbD), is presented in complex with NADP+. This enzyme catalyzes the reduction of dTDP-4-dehydro-β-L-rhamnose to dTDP-β-L-rhamnose. Although the protein was co-crystallized in the presence of Mg2+, the protein lacks the conserved residues that coordinate Mg2+.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-4-dehydrorhamnose reductase
A, B, C, D, E, F
287Bacillus anthracisGene Names: rfbD (spsK)
EC: 1.1.1.133
Find proteins for Q81TN9 (Bacillus anthracis)
Go to UniProtKB:  Q81TN9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 79.449α = 90.00
b = 113.337β = 91.18
c = 144.949γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
Blu-Icedata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-23
    Type: Experimental preparation
  • Version 1.3: 2017-11-08
    Type: Refinement description
  • Version 1.4: 2017-12-13
    Type: Database references