3SMQ

Crystal structure of protein arginine methyltransferase 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An allosteric inhibitor of protein arginine methyltransferase 3.

Siarheyeva, A.Senisterra, G.Allali-Hassani, A.Dong, A.Dobrovetsky, E.Wasney, G.A.Chau, I.Marcellus, R.Hajian, T.Liu, F.Korboukh, I.Smil, D.Bolshan, Y.Min, J.Wu, H.Zeng, H.Loppnau, P.Poda, G.Griffin, C.Aman, A.Brown, P.J.Jin, J.Al-Awar, R.Arrowsmith, C.H.Schapira, M.Vedadi, M.

(2012) Structure 20: 1425-1435

  • DOI: 10.1016/j.str.2012.06.001

  • PubMed Abstract: 
  • PRMT3, a protein arginine methyltransferase, has been shown to influence ribosomal biosynthesis by catalyzing the dimethylation of the 40S ribosomal protein S2. Although PRMT3 has been reported to be a cytosolic protein, it has been shown to methylat ...

    PRMT3, a protein arginine methyltransferase, has been shown to influence ribosomal biosynthesis by catalyzing the dimethylation of the 40S ribosomal protein S2. Although PRMT3 has been reported to be a cytosolic protein, it has been shown to methylate histone H4 peptide (H4 1-24) in vitro. Here, we report the identification of a PRMT3 inhibitor (1-(benzo[d][1,2,3]thiadiazol-6-yl)-3-(2-cyclohexenylethyl)urea; compound 1) with IC50 value of 2.5 μM by screening a library of 16,000 compounds using H4 (1-24) peptide as a substrate. The crystal structure of PRMT3 in complex with compound 1 as well as kinetic analysis reveals an allosteric mechanism of inhibition. Mutating PRMT3 residues within the allosteric site or using compound 1 analogs that disrupt interactions with allosteric site residues both abrogated binding and inhibitory activity. These data demonstrate an allosteric mechanism for inhibition of protein arginine methyltransferases, an emerging class of therapeutic targets.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 3
A
340Homo sapiensMutation(s): 0 
Gene Names: PRMT3 (HRMT1L3)
EC: 2.1.1.-
Find proteins for O60678 (Homo sapiens)
Go to Gene View: PRMT3
Go to UniProtKB:  O60678
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDU
Query on TDU

Download SDF File 
Download CCD File 
A
1-(1,2,3-benzothiadiazol-6-yl)-3-[2-(cyclohex-1-en-1-yl)ethyl]urea
1-(benzo[d][1,2,3]thiadiazol-6-yl)-3-(2-cyclohexenylethyl)urea
C15 H18 N4 O S
GGXCUZHEJUJACD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TDUKd: 9500 nM (99) BINDINGDB
TDUIC50: 1600 - 2400 nM (99) BINDINGDB
TDUKd: 9500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.649α = 90.00
b = 70.649β = 90.00
c = 171.977γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references