6OYY

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report



Literature

The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.

Sun, Q.Li, X.Perez, L.M.Shi, W.Zhang, Y.Sacchettini, J.C.

(2020) Nat Commun 11: 339-339

  • DOI: 10.1038/s41467-019-14238-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug ...

    Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA. sacchett@tamu.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase beta chainA, C, E, G, I, K24Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: panDRv3601cMTCY07H7B.21
EC: 4.1.1.11
Find proteins for P9WIL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIL3 
Go to UniProtKB:  P9WIL3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase alpha chainB, D, F, H, J, L123Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: panDRv3601cMTCY07H7B.21
EC: 4.1.1.11
Find proteins for P9WIL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIL3 
Go to UniProtKB:  P9WIL3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGL
Query on VGL

Download CCD File 
B, D, F, H, J, L
PYRAZINE-2-CARBOXYLIC ACID
C5 H4 N2 O2
NIPZZXUFJPQHNH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.282α = 90
b = 162.282β = 90
c = 62.826γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208
Welch FoundationUnited StatesA-0015

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release