4GWG

Crystal Structure Analysis of 6-phosphogluconate dehydrogenase apo-form

• PDB DOI:  https://doi.org/10.2210/pdb4GWG/pdb

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


• Deposited: 2012-09-03 Released: 2012-11-28 
• Deposition Author(s): He, C., Zhou, L., Zhang, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.186 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth.

Hitosugi, T., Zhou, L., Elf, S., Fan, J., Kang, H.B., Seo, J.H., Shan, C., Dai, Q., Zhang, L., Xie, J., Gu, T.L., Jin, P., Aleckovic, M., Leroy, G., Kang, Y., Sudderth, J.A., Deberardinis, R.J., Luan, C.H., Chen, G.Z., Muller, S., Shin, D.M., Owonikoko, T.K., Lonial, S., Arellano, M.L., Khoury, H.J., Khuri, F.R., Lee, B.H., Ye, K., Boggon, T.J., Kang, S., He, C., Chen, J.

(2012) Cancer Cell 22: 585-600

• PubMed: 23153533 
• DOI: https://doi.org/10.1016/j.ccr.2012.09.020
• Primary Citation of Related Structures:  
  4GWG, 4GWK


• PubMed Abstract: 
  

It is unclear how cancer cells coordinate glycolysis and biosynthesis to support rapidly growing tumors. We found that the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1), commonly upregulated in human cancers due to loss of TP53, contributes to biosynthesis regulation in part by controlling intracellular levels of its substrate, 3-phosphoglycerate (3-PG), and product, 2-phosphoglycerate (2-PG). 3-PG binds to and inhibits 6-phosphogluconate dehydrogenase in the oxidative pentose phosphate pathway (PPP), while 2-PG activates 3-phosphoglycerate dehydrogenase to provide feedback control of 3-PG levels. Inhibition of PGAM1 by shRNA or a small molecule inhibitor PGMI-004A results in increased 3-PG and decreased 2-PG levels in cancer cells, leading to significantly decreased glycolysis, PPP flux and biosynthesis, as well as attenuated cell proliferation and tumor growth.

---

Organizational Affiliation: 

Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.67 kDa 
• Atom Count: 4,301 
• Modelled Residue Count: 467 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, decarboxylating	A	484	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A], C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.186 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.28	α = 90
b = 87.28	β = 90
c = 130.892	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): He, C., Zhou, L., Zhang, L.

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Data collection
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description