4MQQ

Mycobaterium tuberculosis transaminase BioA complexed with benzo[d]thiazole-2-carbohydrazide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibition of Mycobacterium tuberculosis Transaminase BioA by Aryl Hydrazines and Hydrazides.

Dai, R.Wilson, D.J.Geders, T.W.Aldrich, C.C.Finzel, B.C.

(2014) Chembiochem 15: 575-586

  • DOI: https://doi.org/10.1002/cbic.201300748
  • Primary Citation of Related Structures:  
    4CXQ, 4CXR, 4MQP, 4MQQ, 4MQR

  • PubMed Abstract: 

    7,8-Diaminopelargonic acid synthase (BioA) of Mycobacterium tuberculosis is a recently validated target for therapeutic intervention in the treatment of tuberculosis (TB). Using biophysical fragment screening and structural characterization of compounds, we have identified a potent aryl hydrazine inhibitor of BioA that reversibly modifies the pyridoxal-5'-phosphate (PLP) cofactor, forming a stable quinonoid. Analogous hydrazides also form covalent adducts that can be observed crystallographically but are incapable of inactivating the enzyme. In the X-ray crystal structures, small molecules induce unexpected conformational remodeling in the substrate binding site. We compared these conformational changes to those induced upon binding of the substrate (7-keto-8-aminopelargonic acid), and characterized the inhibition kinetics and the X-ray crystal structures of BioA with the hydrazine compound and analogues to unveil the mechanism of this reversible covalent modification.


  • Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN 55455 (USA).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
A, B
457Mycobacterium tuberculosisMutation(s): 0 
Gene Names: bioARv1568MT1619MTCY336.35c
EC: 2.6.1.62
UniProt
Find proteins for P9WQ81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ81 
Go to UniProtKB:  P9WQ81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ81
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2B6
Query on 2B6

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
(4-{[(E)-(1,3-benzothiazol-2-ylcarbonyl)diazenyl]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate
C16 H15 N4 O6 P S
GUGJKPFDBSWCQD-CZIZESTLSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
H [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.948α = 90
b = 66.352β = 90
c = 203.972γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description