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 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1371/journal.pone.0057008
  • Primary Citation of Related Structures:  
    4G56

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hsl7 protein
A, C
657Xenopus laevisMutation(s): 0 
Gene Names: hsl7PRMT5
UniProt
Find proteins for Q6NUA1 (Xenopus laevis)
Explore Q6NUA1 
Go to UniProtKB:  Q6NUA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NUA1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MGC81050 protein
B, D
357Xenopus laevisMutation(s): 0 
Gene Names: MEP50MGC81050wdr77
UniProt
Find proteins for Q6NUD0 (Xenopus laevis)
Explore Q6NUD0 
Go to UniProtKB:  Q6NUD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NUD0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C
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 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.856α = 90
b = 101.935β = 90
c = 125.679γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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