4G56

Crystal Structure of full length PRMT5/MEP50 complexes from Xenopus laevis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity

Ho, M.C.Wilczek, C.Bonanno, J.B.Xing, L.Seznec, J.Matsui, T.Carter, L.G.Onikubo, T.Kumar, P.R.Chan, M.K.Brenowitz, M.Cheng, R.H.Reimer, U.Almo, S.C.Shechter, D.

(2013) Plos One 8: e57008-e57008

  • DOI: 10.1371/journal.pone.0057008

  • PubMed Abstract: 
  • The arginine methyltransferase PRMT5-MEP50 is required for embryogenesis and is misregulated in many cancers. PRMT5 targets a wide variety of substrates, including histone proteins involved in specifying an epigenetic code. However, the mechanism by ...

    The arginine methyltransferase PRMT5-MEP50 is required for embryogenesis and is misregulated in many cancers. PRMT5 targets a wide variety of substrates, including histone proteins involved in specifying an epigenetic code. However, the mechanism by which PRMT5 utilizes MEP50 to discriminate substrates and to specifically methylate target arginines is unclear. To test a model in which MEP50 is critical for substrate recognition and orientation, we determined the crystal structure of Xenopus laevis PRMT5-MEP50 complexed with S-adenosylhomocysteine (SAH). PRMT5-MEP50 forms an unusual tetramer of heterodimers with substantial surface negative charge. MEP50 is required for PRMT5-catalyzed histone H2A and H4 methyltransferase activity and binds substrates independently. The PRMT5 catalytic site is oriented towards the cross-dimer paired MEP50. Histone peptide arrays and solution assays demonstrate that PRMT5-MEP50 activity is inhibited by substrate phosphorylation and enhanced by substrate acetylation. Electron microscopy and reconstruction showed substrate centered on MEP50. These data support a mechanism in which MEP50 binds substrate and stimulates PRMT5 activity modulated by substrate post-translational modifications.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America. joeho@gate.sinica.edu.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hsl7 protein
A, C
657Xenopus laevisMutation(s): 0 
Gene Names: prmt5 (hsl7)
EC: 2.1.1.320
Find proteins for Q6NUA1 (Xenopus laevis)
Go to UniProtKB:  Q6NUA1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MGC81050 protein
B, D
357Xenopus laevisMutation(s): 0 
Gene Names: wdr77 (mep50)
Find proteins for Q6NUD0 (Xenopus laevis)
Go to UniProtKB:  Q6NUD0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, C
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 181.856α = 90.00
b = 101.935β = 90.00
c = 125.679γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Derived calculations
  • Version 1.2: 2013-03-13
    Type: Database references
  • Version 1.3: 2013-09-04
    Type: Database references
  • Version 1.4: 2013-09-11
    Type: Other
  • Version 1.5: 2017-11-15
    Type: Refinement description