4QQK

Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) with GMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of arginine asymmetrical dimethylation by PRMT6.

Wu, H.Zheng, W.Eram, M.S.Vhuiyan, M.Dong, A.Zeng, H.He, H.Brown, P.Frankel, A.Vedadi, M.Luo, M.Min, J.

(2016) Biochem. J. 473: 3049-3063

  • DOI: 10.1042/BCJ20160537
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PRMT6 is a type I protein arginine methyltransferase, generating the asymmetric dimethylarginine mark on proteins such as histone H3R2. Asymmetric dimethylation of histone H3R2 by PRMT6 acts as a repressive mark that antagonizes trimethylation of H3 ...

    PRMT6 is a type I protein arginine methyltransferase, generating the asymmetric dimethylarginine mark on proteins such as histone H3R2. Asymmetric dimethylation of histone H3R2 by PRMT6 acts as a repressive mark that antagonizes trimethylation of H3 lysine 4 by the MLL histone H3K4 methyltransferase. PRMT6 is overexpressed in several cancer types, including prostate, bladder and lung cancers; therefore, it is of great interest to develop potent and selective inhibitors for PRMT6. Here, we report the synthesis of a potent bisubstrate inhibitor GMS [6'-methyleneamine sinefungin, an analog of sinefungin (SNF)], and the crystal structures of human PRMT6 in complex, respectively, with S-adenosyl-L-homocysteine (SAH) and the bisubstrate inhibitor GMS that shed light on the significantly improved inhibition effect of GMS on methylation activity of PRMT6 compared with SAH and an S-adenosyl-L-methionine competitive methyltransferase inhibitor SNF. In addition, we also crystallized PRMT6 in complex with SAH and a short arginine-containing peptide. Based on the structural information here and available in the PDB database, we proposed a mechanism that can rationalize the distinctive arginine methylation product specificity of different types of arginine methyltransferases and pinpoint the structural determinant of such a specificity.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada.,Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, N.Y 10065, U.S.A.,Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 6
A
376Homo sapiensMutation(s): 1 
Gene Names: PRMT6 (HRMT1L6)
EC: 2.1.1.319
Find proteins for Q96LA8 (Homo sapiens)
Go to Gene View: PRMT6
Go to UniProtKB:  Q96LA8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
37H
Query on 37H

Download SDF File 
Download CCD File 
A
(5S)-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}-N~6~-carbamimidoyl-L-lysine
C17 H27 N9 O5
PRQKNHVENSAKGM-TVDBPQCTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 95.211α = 90.00
b = 95.211β = 90.00
c = 108.359γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
HKL-3000data scaling
Cootmodel building
SCALEPACKdata scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references