8GWR

Near full length Kidney type Glutaminase in complex with 2,2-Dimethyl-2,3-Dihydrobenzo[a] Phenanthridin-4(1H)-one (DDP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

A novel allosteric site employs a conserved inhibition mechanism in human kidney-type glutaminase.

Shankar, S.Ramachandran, S.Tulsian, N.Radhakrishnan, S.Jobichen, C.Sivaraman, J.

(2023) FEBS J 290: 2437-2448

  • DOI: https://doi.org/10.1111/febs.16658
  • Primary Citation of Related Structures:  
    8GWR

  • PubMed Abstract: 

    Glutaminase catalyses the metabolic process called glutaminolysis. Cancer cells harness glutaminolysis to increase energy reserves under stressful conditions for rapid proliferation. Glutaminases are upregulated in many tumours. In humans, the kidney-type glutaminase (KGA) isoform is highly expressed in the kidney, brain, intestine, foetal liver, lymphocytes and in many tumours. Glutaminase inhibition is shown to be effective in controlling cancers. Previously, we and others reported the inhibition mechanism of KGA using various inhibitors that target the active and allosteric sites of the enzyme. Here, we report the identification of a novel allosteric site in KGA using the compound DDP through its complex crystal structure combined with mutational and hydrogen-deuterium exchange mass spectrometry studies. This allosteric site is located at the dimer interface, situated ~ 31 Å away from the previously identified allosteric site and ~ 32 Å away from the active site. Remarkably, the mechanism of inhibition is conserved, irrespective of which allosteric pocket is targeted, causing the same conformational changes in the key loop near the active site (Glu312-Pro329) and subsequent enzyme inactivation. Contrary to the previously identified allosteric site, the identified new allosteric site is primarily hydrophilic. This site could be effectively targeted for the synthesis of specific and potent water-soluble inhibitors of glutaminase, which will lead to the development of anticancer drugs.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrialA [auth B],
B [auth A]
669Homo sapiensMutation(s): 0 
Gene Names: GLSGLS1KIAA0838
EC: 3.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O94925 (Homo sapiens)
Explore O94925 
Go to UniProtKB:  O94925
PHAROS:  O94925
GTEx:  ENSG00000115419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94925
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HZO
Query on HZO

Download Ideal Coordinates CCD File 
C [auth B]2,2-dimethyl-1,3-dihydrobenzo[a]phenanthridin-4-one
C19 H17 N O
VFHPHBGZIZTJDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.194α = 90
b = 143.194β = 90
c = 167.488γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeR154-000-A72-114

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description