4EDU

The MBT repeats of human SCML2 in a complex with histone H2A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Histone recognition by human malignant brain tumor domains.

Nady, N.Krichevsky, L.Zhong, N.Duan, S.Tempel, W.Amaya, M.F.Ravichandran, M.Arrowsmith, C.H.

(2012) J.Mol.Biol. 423: 702-718

  • DOI: 10.1016/j.jmb.2012.08.022

  • PubMed Abstract: 
  • Histone methylation has emerged as an important covalent modification involved in a variety of biological processes, especially regulation of transcription and chromatin dynamics. Lysine methylation is found in three distinct states (monomethylation, ...

    Histone methylation has emerged as an important covalent modification involved in a variety of biological processes, especially regulation of transcription and chromatin dynamics. Lysine methylation is found in three distinct states (monomethylation, dimethylation and trimethylation), which are recognized by specific protein domains. The malignant brain tumor (MBT) domain is one such module found in several chromatin regulatory complexes including Polycomb repressive complex 1. Here, we present a comprehensive characterization of the human MBT family with emphasis on histone binding specificity. SPOT-blot peptide arrays were used to screen for the methyllysine-containing histone peptides that bind to MBT domains found in nine human proteins. Selected interactions were quantified using fluorescence polarization assays. We show that all MBT proteins recognize only monomethyllysine and/or dimethyllysine marks and provide evidence that some MBT domains recognize a defined consensus sequence while others bind in a promiscuous, non-sequence-specific manner. Furthermore, using structure-based mutants, we identify a triad of residues in the methyllysine binding pocket that imparts discrimination between monomethyllysine and dimethyllysine. This study represents a comprehensive analysis of MBT substrate specificity, establishing a foundation for the rational design of selective MBT domain inhibitors that may enable elucidation of their role in human biology and disease.


    Organizational Affiliation

    Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada M5G 1L7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sex comb on midleg-like protein 2
A
215Homo sapiensMutation(s): 1 
Gene Names: SCML2
Find proteins for Q9UQR0 (Homo sapiens)
Go to Gene View: SCML2
Go to UniProtKB:  Q9UQR0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.J peptide
T
16Homo sapiensMutation(s): 0 
Gene Names: H2AFJ
Find proteins for Q9BTM1 (Homo sapiens)
Go to Gene View: H2AFJ
Go to UniProtKB:  Q9BTM1
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
T
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.949α = 90.00
b = 69.949β = 90.00
c = 169.609γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description