2WHI

Crystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with a purine analogue inhibitor and L-methionine-S- sulfoximine phosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for the Inhibition of Mycobacterium Tuberculosis Glutamine Synthetase by Novel ATP-Competitive Inhibitors.

Nilsson, M.T.Krajewski, W.W.Yellagunda, S.Prabhumurthy, S.Chamarahally, G.N.Siddamadappa, C.Srinivasa, B.R.Yahiaoui, S.Larhed, M.Karlen, A.Jones, T.A.Mowbray, S.L.

(2009) J Mol Biol 393: 504

  • DOI: https://doi.org/10.1016/j.jmb.2009.08.028
  • Primary Citation of Related Structures:  
    2WGS, 2WHI

  • PubMed Abstract: 

    Glutamine synthetase (GS, EC 6.3.1.2; also known as gamma-glutamyl:ammonia ligase) catalyzes the ATP-dependent condensation of glutamate and ammonia to form glutamine. The enzyme has essential roles in different tissues and species, which have led to its consideration as a drug or an herbicide target. In this article, we describe studies aimed at the discovery of new antimicrobial agents targeting Mycobacterium tuberculosis, the causative pathogen of tuberculosis. A number of distinct classes of GS inhibitors with an IC(50) of micromolar value or better were identified via high-throughput screening. A commercially available purine analogue similar to one of the clusters identified (the diketopurines), 1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-8-morpholin-4-yl-purine-2,6-dione, was also shown to inhibit the enzyme, with a measured IC(50) of 2.5+/-0.4 microM. Two X-ray structures are presented: one is a complex of the enzyme with the purine analogue alone (2.55-A resolution), and the other includes the compound together with methionine sulfoximine phosphate, magnesium and phosphate (2.2-A resolution). The former represents a relaxed, inactive conformation of the enzyme, while the latter is a taut, active one. These structures show that the compound binds at the same position in the nucleotide site, regardless of the conformational state. The ATP-binding site of the human enzyme differs substantially, explaining why it has an approximately 60-fold lower affinity for this compound than the bacterial GS. As part of this work, we devised a new synthetic procedure for generating l-(SR)-methionine sulfoximine phosphate from l-(SR)-methionine sulfoximine, which will facilitate future investigations of novel GS inhibitors.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMINE SYNTHETASE 1
A, B, C, D, E
A, B, C, D, E, F
486Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 6.3.1.2
UniProt
Find proteins for P9WN39 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN39 
Go to UniProtKB:  P9WN39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN39
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1AZ
Query on 1AZ

Download Ideal Coordinates CCD File 
EA [auth D]
G [auth A]
MA [auth E]
O [auth B]
UA [auth F]
EA [auth D],
G [auth A],
MA [auth E],
O [auth B],
UA [auth F],
W [auth C]
1-(3,4-dichlorobenzyl)-3,7-dimethyl-8-morpholin-4-yl-3,7-dihydro-1H-purine-2,6-dione
C18 H19 Cl2 N5 O3
BFRVAZYYGGLHQS-UHFFFAOYSA-N
P3S
Query on P3S

Download Ideal Coordinates CCD File 
AA [auth C]
IA [auth D]
K [auth A]
QA [auth E]
S [auth B]
AA [auth C],
IA [auth D],
K [auth A],
QA [auth E],
S [auth B],
YA [auth F]
L-METHIONINE-S-SULFOXIMINE PHOSPHATE
C5 H13 N2 O6 P S
QQFOFBSCSWFFPB-NMAPHRJESA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
BB [auth F]
DA [auth C]
LA [auth D]
N [auth A]
TA [auth E]
BB [auth F],
DA [auth C],
LA [auth D],
N [auth A],
TA [auth E],
V [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth C]
JA [auth D]
L [auth A]
RA [auth E]
T [auth B]
BA [auth C],
JA [auth D],
L [auth A],
RA [auth E],
T [auth B],
ZA [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth F]
CA [auth C]
KA [auth D]
M [auth A]
SA [auth E]
AB [auth F],
CA [auth C],
KA [auth D],
M [auth A],
SA [auth E],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth D]
GA [auth D]
H [auth A]
HA [auth D]
I [auth A]
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
J [auth A],
NA [auth E],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
R [auth B],
VA [auth F],
WA [auth F],
X [auth C],
XA [auth F],
Y [auth C],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.21α = 90
b = 228.76β = 90
c = 202.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description