4GWK

Crystal structure of 6-phosphogluconate dehydrogenase complexed with 3-phosphoglyceric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.534 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1016/j.ccr.2012.09.020
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconate dehydrogenase, decarboxylating
A
484Homo sapiensMutation(s): 0 
Gene Names: PGD (PGDH)
EC: 1.1.1.44
Find proteins for P52209 (Homo sapiens)
Go to Gene View: PGD
Go to UniProtKB:  P52209
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3PGKi: 489000 nM BINDINGMOAD
3PGKd: 460000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.534 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.246α = 90.00
b = 87.246β = 90.00
c = 130.424γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASESphasing
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release