2BPQ

Anthranilate phosphoribosyltransferase (TrpD) from Mycobacterium tuberculosis (Apo structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crystal Structure of Trpd, a Metabolic Enzyme Essential for Lung Colonization by Mycobacterium Tuberculosis, in Complex with its Substrate Phosphoribosylpyrophosphate

Lee, C.E.Goodfellow, C.Javid-Majd, F.Baker, E.N.Lott, J.S.

(2006) J.Mol.Biol. 355: 784

  • DOI: 10.1016/j.jmb.2005.11.016
  • Primary Citation of Related Structures:  1ZVW

  • PubMed Abstract: 
  • Mycobacterium tuberculosis, the cause of tuberculosis, presents a major threat to human health worldwide. Biosynthetic enzymes that are essential for the survival of the bacterium, especially in activated macrophages, are important potential drug tar ...

    Mycobacterium tuberculosis, the cause of tuberculosis, presents a major threat to human health worldwide. Biosynthetic enzymes that are essential for the survival of the bacterium, especially in activated macrophages, are important potential drug targets. Although the tryptophan biosynthesis pathway is thought to be non-essential for many pathogens, this appears not to be the case for M.tuberculosis, where a trpD gene knockout fails to cause disease in mice. We therefore chose the product of the trpD gene, anthranilate phosphoribosyltransferase, which catalyses the second step in tryptophan biosynthesis, for structural analysis. The structure of TrpD from M.tuberculosis was solved by X-ray crystallography, at 1.9 A resolution for the native enzyme (R = 0.191, Rfree = 0.230) and at 2.3 A resolution for the complex with its substrate phosphoribosylpyrophosphate (PRPP) and Mg2+ (R = 0.194, Rfree = 0.255). The enzyme is folded into two domains, separated by a hinge region. PRPP binds in the C-terminal domain, together with a pair of Mg ions. In the substrate complex, two flexible loops change conformation compared with the apo protein, to close over the PRPP and to complete an extensive network of hydrogen-bonded interactions. A nearby pocket, adjacent to the hinge region, is postulated by in silico docking as the binding site for anthranilate. A bound molecule of benzamidine, which was essential for crystallization and is also found in the hinge region, appears to reduce flexibility between the two domains.


    Organizational Affiliation

    Laboratory of Structural Biology and Centre for Molecular Biodiscovery, School of Biological Sciences University of Auckland, Private Bag 92019, Auckland 1020, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
A, B
373Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Gene Names: trpD
EC: 2.4.2.18
Find proteins for P9WFX4 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WFX4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A, B
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.874α = 90.00
b = 82.415β = 90.00
c = 117.520γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-04
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Derived calculations, Non-polymer description, Other, Version format compliance