2R5A

Crystal Structure of the two MBT repeats from Sex-Comb on Midleg (SCM) in complex with methyl lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg.

Grimm, C.de Ayala Alonso, A.G.Rybin, V.Steuerwald, U.Ly-Hartig, N.Fischle, W.Muller, J.Muller, C.W.

(2007) Embo Rep. 8: 1031-1037

  • DOI: 10.1038/sj.embor.7401085
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sex comb on midleg (Scm) is a member of the Polycomb group of proteins involved in the maintenance of repression of Hox and other developmental control genes in Drosophila. The two malignant brain tumour (MBT) repeats of Scm form a domain that prefer ...

    Sex comb on midleg (Scm) is a member of the Polycomb group of proteins involved in the maintenance of repression of Hox and other developmental control genes in Drosophila. The two malignant brain tumour (MBT) repeats of Scm form a domain that preferentially binds to monomethylated lysine residues either as a free amino acid or in the context of peptides, while unmodified or di- or trimethylated lysine residues are bound with significantly lower affinity. The crystal structure of a monomethyl-lysine-containing histone tail peptide bound to the MBT repeat domain shows that the methyl-lysine side chain occupies a binding pocket in the second MBT repeat formed by three conserved aromatic residues and one aspartate. Insertion of the monomethylated side chain into this pocket seems to be the main contributor to the binding affinity. Functional analyses in Drosophila show that the MBT domain of Scm and its methyl-lysine-binding activity are required for repression of Hox genes.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein Scm
A
265Drosophila melanogasterMutation(s): 1 
Gene Names: Scm
Find proteins for Q9VHA0 (Drosophila melanogaster)
Go to UniProtKB:  Q9VHA0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLZ
Query on MLZ

Download SDF File 
Download CCD File 
A
N-METHYL-LYSINE
C7 H16 N2 O2
PQNASZJZHFPQLE-LURJTMIESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MLZKd: 2500000 nM BINDINGMOAD
MLZKd: 2500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.030α = 90.00
b = 83.030β = 90.00
c = 75.790γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
DNAdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance