2Y88

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE (VARIANT D11N) WITH BOUND PRFAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bisubstrate Specificity in Histidine/Tryptophan Biosynthesis Isomerase from Mycobacterium Tuberculosis by Active Site Metamorphosis.

Due, A.V.Kuper, J.Geerlof, A.Kries, J.P.Wilmanns, M.

(2011) Proc.Natl.Acad.Sci.USA 108: 3554

  • DOI: 10.1073/pnas.1015996108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In histidine and tryptophan biosynthesis, two related isomerization reactions are generally catalyzed by two specific single-substrate enzymes (HisA and TrpF), sharing a similar (β/α)(8)-barrel scaffold. However, in some actinobacteria, one of the tw ...

    In histidine and tryptophan biosynthesis, two related isomerization reactions are generally catalyzed by two specific single-substrate enzymes (HisA and TrpF), sharing a similar (β/α)(8)-barrel scaffold. However, in some actinobacteria, one of the two encoding genes (trpF) is missing and the two reactions are instead catalyzed by one bisubstrate enzyme (PriA). To unravel the unknown mechanism of bisubstrate specificity, we used the Mycobacterium tuberculosis PriA enzyme as a model. Comparative structural analysis of the active site of the enzyme showed that PriA undergoes a reaction-specific and substrate-induced metamorphosis of the active site architecture, demonstrating its unique ability to essentially form two different substrate-specific actives sites. Furthermore, we found that one of the two catalytic residues in PriA, which are identical in both isomerization reactions, is recruited by a substrate-dependent mechanism into the active site to allow its involvement in catalysis. Comparison of the structural data from PriA with one of the two single-substrate enzymes (TrpF) revealed substantial differences in the active site architecture, suggesting independent evolution. To support these observations, we identified six small molecule compounds that inhibited both PriA-catalyzed isomerization reactions but had no effect on TrpF activity. Our data demonstrate an opportunity for organism-specific inhibition of enzymatic catalysis by taking advantage of the distinct ability for bisubstrate catalysis in the M. tuberculosis enzyme.


    Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHORIBOSYL ISOMERASE A
A
244Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 1 
Gene Names: priA (hisA)
Find proteins for P9WMM4 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WMM4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2ER
Query on 2ER

Download SDF File 
Download CCD File 
A
[(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[[(Z)-[(3R,4R)-3,4-DIHYDROXY-2-OXO-5-PHOSPHONOOXY-PENTYL]IMINOMETHYL]AMINO]IMIDAZOL-1-YL]-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
C15 H25 N5 O15 P2
BLKFNHOCHNCLII-GHVQHMAVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.138 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.270α = 90.00
b = 63.270β = 90.00
c = 131.220γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance