5UQ9 | pdb_00005uq9

Crystal structure of 6-phosphogluconate dehydrogenase with ((4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl)methyl dihydrogen phosphate

• PDB DOI: https://doi.org/10.2210/pdb5UQ9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-07 Released: 2018-08-22 
• Deposition Author(s): Leonard, P.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.272 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Functional Genomics Reveals Synthetic Lethality between Phosphogluconate Dehydrogenase and Oxidative Phosphorylation.

Sun, Y., Bandi, M., Lofton, T., Smith, M., Bristow, C.A., Carugo, A., Rogers, N., Leonard, P., Chang, Q., Mullinax, R., Han, J., Shi, X., Seth, S., Meyers, B.A., Miller, M., Miao, L., Ma, X., Feng, N., Giuliani, V., Geck Do, M., Czako, B., Palmer, W.S., Mseeh, F., Asara, J.M., Jiang, Y., Morlacchi, P., Zhao, S., Peoples, M., Tieu, T.N., Warmoes, M.O., Lorenzi, P.L., Muller, F.L., DePinho, R.A., Draetta, G.F., Toniatti, C., Jones, P., Heffernan, T.P., Marszalek, J.R.

(2019) Cell Rep 26: 469-482.e5

• PubMed: 30625329 
• DOI: https://doi.org/10.1016/j.celrep.2018.12.043
• Primary Citation Related Structures: 
  5UQ9


• PubMed Abstract: 
  

  The plasticity of a preexisting regulatory circuit compromises the effectiveness of targeted therapies, and leveraging genetic vulnerabilities in cancer cells may overcome such adaptations. Hereditary leiomyomatosis renal cell carcinoma (HLRCC) is characterized by oxidative phosphorylation (OXPHOS) deficiency caused by fumarate hydratase (FH) nullizyogosity. To identify metabolic genes that are synthetically lethal with OXPHOS deficiency, we conducted a genetic loss-of-function screen and found that phosphogluconate dehydrogenase (PGD) inhibition robustly blocks the proliferation of FH mutant cancer cells both in vitro and in vivo. Mechanistically, PGD inhibition blocks glycolysis, suppresses reductive carboxylation of glutamine, and increases the NADP ⁺ /NADPH ratio to disrupt redox homeostasis. Furthermore, in the OXPHOS-proficient context, blocking OXPHOS using the small-molecule inhibitor IACS-010759 enhances sensitivity to PGD inhibition in vitro and in vivo. Together, our study reveals a dependency on PGD in OXPHOS-deficient tumors that might inform therapeutic intervention in specific patient populations.

---

Organizational Affiliation: 
• Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: [e-mail].
Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 430.38 kDa 
• Atom Count: 29,092 
• Modeled Residue Count: 3,746 
• Deposited Residue Count: 3,912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, decarboxylating	A, B, C, D, E, F, G, H	489	Homo sapiens	Mutation(s): 0  Gene Names: PGD, PGDH EC: 1.1.1.44
UniProt & NIH Common Fund Data Resources
Find proteins for P52209 (Homo sapiens) Explore P52209  Go to UniProtKB:  P52209
PHAROS:  P52209 GTEx:  ENSG00000142657

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8HS	I [auth F]	[(4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl dihydrogen phosphate C7 H14 N O8 P DVFAQEVWJBLFDS-RFZPGFLSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8HS	BindingDB:  5UQ9	Ki: min: 35, max: 1100 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.272 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.311	α = 90
b = 164.93	β = 91.43
c = 133.199	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Leonard, P.G.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description