3UO9

Crystal Structure of Human GAC in Complex with Glutamate and BPTES

• PDB DOI: https://doi.org/10.2210/pdb3UO9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-11-16 Released: 2011-12-07 
• Deposition Author(s): DeLaBarre, B., Gross, S., Cheng, F., Gao, Y., Jha, A., Jiang, F., Song, J.J., Wei, W., Hurov, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.249 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Full-length human glutaminase in complex with an allosteric inhibitor.

DeLaBarre, B., Gross, S., Fang, C., Gao, Y., Jha, A., Jiang, F., Song J, J., Wei, W., Hurov, J.B.

(2011) Biochemistry 50: 10764-10770

• PubMed: 22049910 
• DOI: https://doi.org/10.1021/bi201613d
• Primary Citation of Related Structures:  
  3UNW, 3UO9


• PubMed Abstract: 
  

  Glutaminase (GLS1/2) catalyzes the conversion of L-glutamine to L-glutamate and ammonia. The level of a splice variant of GLS1 (GAC) is elevated in certain cancers, and GAC is specifically inhibited by bis-2-(5-phenylacetimido-1,2,4,thiadiazol-2-yl)ethyl sulfide (BPTES). We report here the first full-length crystal structure of GAC in the presence and absence of BPTES molecules. Two BPTES molecules bind at an interface region of the GAC tetramer in a manner that appears to lock the GAC tetramer into a nonproductive conformation. The importance of these loops with regard to overall enzymatic activity of the tetramer was revealed by a series of GAC point mutants designed to create a BPTES resistant GAC.

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Organizational Affiliation: 

Agios Pharmaceuticals, Cambridge, Massachusetts 02139-4169, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 237.17 kDa 
• Atom Count: 13,319 
• Modelled Residue Count: 1,624 
• Deposited Residue Count: 2,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminase kidney isoform, mitochondrial	A, B, C, D	534	Homo sapiens	Mutation(s): 0  Gene Names: GLS, GLS1, KIAA0838 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
04A	G [auth B], H [auth C]	N,N'-[sulfanediylbis(ethane-2,1-diyl-1,3,4-thiadiazole-5,2-diyl)]bis(2-phenylacetamide) C24 H24 N6 O2 S3 MDJIPXYRSZHCFS-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], I [auth C], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
04A	BindingDB:  3UO9	Kd: min: 200, max: 4300 (nM) from 2 assay(s)
		IC50: min: 25, max: 8600 (nM) from 15 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.249 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.117	α = 90
b = 139.434	β = 93.73
c = 177.713	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): DeLaBarre, B., Gross, S., Cheng, F., Gao, Y., Jha, A., Jiang, F., Song, J.J., Wei, W., Hurov, J.B.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references