6P02

Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1038/s41467-019-14238-3
  • Primary Citation of Related Structures:  
    6OYY, 6OZ8, 6P02, 6P1Y

  • 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 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.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate 1-decarboxylase beta chain
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
24Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: panDRv3601cMTCY07H7B.21
UniProt
Find proteins for P9WIL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIL3 
Go to UniProtKB:  P9WIL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIL3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate 1-decarboxylase alpha chain
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
123Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: panDRv3601cMTCY07H7B.21
EC: 4.1.1.11
UniProt
Find proteins for P9WIL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIL3 
Go to UniProtKB:  P9WIL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIL3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMJ (Subject of Investigation/LOI)
Query on NMJ

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth H]
CA [auth J]
DA [auth L]
EA [auth N]
AA [auth F],
BA [auth H],
CA [auth J],
DA [auth L],
EA [auth N],
FA [auth P],
GA [auth R],
HA [auth T],
IA [auth V],
JA [auth X],
Y [auth B],
Z [auth D]
6-chloropyrazine-2-carboxylic acid
C5 H3 Cl N2 O2
KGGYMBKTQCLOTE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NMJ Binding MOAD:  6P02 Ki: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.679α = 90
b = 143.679β = 90
c = 59.838γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations