5FA5

Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5.

Mavrakis, K.J., McDonald, E.R., Schlabach, M.R., Billy, E., Hoffman, G.R., deWeck, A., Ruddy, D.A., Venkatesan, K., Yu, J., McAllister, G., Stump, M., deBeaumont, R., Ho, S., Yue, Y., Liu, Y., Yan-Neale, Y., Yang, G., Lin, F., Yin, H., Gao, H., Kipp, D.R., Zhao, S., McNamara, J.T., Sprague, E.R., Zheng, B., Lin, Y., Cho, Y.S., Gu, J., Crawford, K., Ciccone, D., Vitari, A.C., Lai, A., Capka, V., Hurov, K., Porter, J.A., Tallarico, J., Mickanin, C., Lees, E., Pagliarini, R., Keen, N., Schmelzle, T., Hofmann, F., Stegmeier, F., Sellers, W.R.

(2016) Science 351: 1208-1213

  • DOI: 10.1126/science.aad5944

  • PubMed Abstract: 

    • 5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a ...

    5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a large-scale short hairpin RNA-mediated screen across 390 cancer cell line models, we found that the viability of MTAP-deficient cancer cells is impaired by depletion of the protein arginine methyltransferase PRMT5. MTAP-deleted cells accumulate the metabolite methylthioadenosine (MTA), which we found to inhibit PRMT5 methyltransferase activity. Deletion of MTAP in MTAP-proficient cells rendered them sensitive to PRMT5 depletion. Conversely, reconstitution of MTAP in an MTAP-deficient cell line rescued PRMT5 dependence. Thus, MTA accumulation in MTAP-deleted cancers creates a hypomorphic PRMT5 state that is selectively sensitized toward further PRMT5 inhibition. Inhibitors of PRMT5 that leverage this dysregulated metabolic state merit further investigation as a potential therapy for MTAP/CDKN2A-deleted tumors.

    Organizational Affiliation: 

    Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 5
A
650Homo sapiensMutation(s): 0 
Gene Names: PRMT5 (HRMT1L5, IBP72, JBP1, SKB1)
EC: 2.1.1.320
Find proteins for O14744 (Homo sapiens)
Go to Gene View: PRMT5
Go to UniProtKB:  O14744
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methylosome protein 50
B
367Homo sapiensMutation(s): 0 
Gene Names: WDR77 (MEP50, WD45)
Find proteins for Q9BQA1 (Homo sapiens)
Go to Gene View: WDR77
Go to UniProtKB:  Q9BQA1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C
20Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4
Go to UniProtKB:  P62805
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA
Download SDF File 
Download CCD File 
A
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTAIC50: 4600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.050α = 90.00
b = 137.850β = 90.00
c = 178.430γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2016-03-23
    Type: Database references