3VP2

Crystal structure of human glutaminase in complex with inhibitor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the allosteric inhibitory mechanism of human kidney-type glutaminase (KGA) and its regulation by Raf-Mek-Erk signaling in cancer cell metabolism.

Thangavelu, K.Pan, C.Q.Karlberg, T.Balaji, G.Uttamchandani, M.Suresh, V.Schuler, H.Low, B.C.Sivaraman, J.

(2012) Proc.Natl.Acad.Sci.USA 109: 7705-7710

  • DOI: 10.1073/pnas.1116573109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Besides thriving on altered glucose metabolism, cancer cells undergo glutaminolysis to meet their energy demands. As the first enzyme in catalyzing glutaminolysis, human kidney-type glutaminase isoform (KGA) is becoming an attractive target for small ...

    Besides thriving on altered glucose metabolism, cancer cells undergo glutaminolysis to meet their energy demands. As the first enzyme in catalyzing glutaminolysis, human kidney-type glutaminase isoform (KGA) is becoming an attractive target for small molecules such as BPTES [bis-2-(5 phenylacetamido-1, 2, 4-thiadiazol-2-yl) ethyl sulfide], although the regulatory mechanism of KGA remains unknown. On the basis of crystal structures, we reveal that BPTES binds to an allosteric pocket at the dimer interface of KGA, triggering a dramatic conformational change of the key loop (Glu312-Pro329) near the catalytic site and rendering it inactive. The binding mode of BPTES on the hydrophobic pocket explains its specificity to KGA. Interestingly, KGA activity in cells is stimulated by EGF, and KGA associates with all three kinase components of the Raf-1/Mek2/Erk signaling module. However, the enhanced activity is abrogated by kinase-dead, dominant negative mutants of Raf-1 (Raf-1-K375M) and Mek2 (Mek2-K101A), protein phosphatase PP2A, and Mek-inhibitor U0126, indicative of phosphorylation-dependent regulation. Furthermore, treating cells that coexpressed Mek2-K101A and KGA with suboptimal level of BPTES leads to synergistic inhibition on cell proliferation. Consequently, mutating the crucial hydrophobic residues at this key loop abrogates KGA activity and cell proliferation, despite the binding of constitutive active Mek2-S222/226D. These studies therefore offer insights into (i) allosteric inhibition of KGA by BPTES, revealing the dynamic nature of KGA's active and inhibitory sites, and (ii) cross-talk and regulation of KGA activities by EGF-mediated Raf-Mek-Erk signaling. These findings will help in the design of better inhibitors and strategies for the treatment of cancers addicted with glutamine metabolism.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore 117543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaminase kidney isoform, mitochondrial
A
315Homo sapiensMutation(s): 0 
Gene Names: GLS (GLS1, KIAA0838)
EC: 3.5.1.2
Find proteins for O94925 (Homo sapiens)
Go to Gene View: GLS
Go to UniProtKB:  O94925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BP0
Query on BP0

Download SDF File 
Download CCD File 
A
5,5'-(sulfanediyldiethane-2,1-diyl)bis(1,3,4-thiadiazol-2-amine)
C8 H12 N6 S3
AOAQKDDVWLOZFV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BP0IC50: 100000 nM (99) BINDINGDB
BP0IC50: 8020 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.883α = 90.00
b = 139.883β = 90.00
c = 158.005γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Structure summary