5UQ9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1016/j.celrep.2018.12.043
  • Primary Citation of 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 ...

    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: jrmarszalek@mdanderson.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, decarboxylatingA, B, C, D, E, F, G, H489Homo sapiensMutation(s): 0 
Gene Names: PGDPGDH
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8HS
Query on 8HS

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.311α = 90
b = 164.93β = 91.43
c = 133.199γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references