4OWS

Anthranilate phosphoribosyl transferase from Mycobacterium tuberculosis in complex with 4-methylanthranilate, PRPP and Magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis.

Cookson, T.V.Castell, A.Bulloch, E.M.Evans, G.L.Short, F.L.Baker, E.N.Lott, J.S.Parker, E.J.

(2014) Biochem.J. 461: 87-98

  • DOI: 10.1042/BJ20140209
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AnPRT (anthranilate phosphoribosyltransferase), required for the biosynthesis of tryptophan, is essential for the virulence of Mycobacterium tuberculosis (Mtb). AnPRT catalyses the Mg2+-dependent transfer of a phosphoribosyl group from PRPP (5'-phosp ...

    AnPRT (anthranilate phosphoribosyltransferase), required for the biosynthesis of tryptophan, is essential for the virulence of Mycobacterium tuberculosis (Mtb). AnPRT catalyses the Mg2+-dependent transfer of a phosphoribosyl group from PRPP (5'-phosphoribosyl-1'-pyrophosphate) to anthranilate to form PRA (5'-phosphoribosyl anthranilate). Mtb-AnPRT was shown to catalyse a sequential reaction and significant substrate inhibition by anthranilate was observed. Antimycobacterial fluoroanthranilates and methyl-substituted analogues were shown to act as alternative substrates for Mtb-AnPRT, producing the corresponding substituted PRA products. Structures of the enzyme complexed with anthranilate analogues reveal two distinct binding sites for anthranilate. One site is located over 8 Å (1 Å=0.1 nm) from PRPP at the entrance to a tunnel leading to the active site, whereas in the second, inner, site anthranilate is adjacent to PRPP, in a catalytically relevant position. Soaking the analogues for variable periods of time provides evidence for anthranilate located at transient positions during transfer from the outer site to the inner catalytic site. PRPP and Mg2+ binding have been shown to be associated with the rearrangement of two flexible loops, which is required to complete the inner anthranilate-binding site. It is proposed that anthranilate first binds to the outer site, providing an unusual mechanism for substrate capture and efficient transfer to the catalytic site following the binding of PRPP.


    Organizational Affiliation

    *Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140, New Zealand.,†Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anthranilate phosphoribosyltransferase
A, B
378Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: trpD
EC: 2.4.2.18
Find proteins for P9WFX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFX5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
4M0
Query on 4M0

Download SDF File 
Download CCD File 
A, B
2-azanyl-4-methyl-benzoic acid
4-methylanthranilate
C8 H9 N O2
RPGKFFKUTVJVPY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.726α = 90.00
b = 91.780β = 90.00
c = 120.567γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Data collection
  • Version 1.3: 2017-09-27
    Type: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2018-03-07
    Type: Data collection