3F70

Crystal structure of L3MBTL2-H4K20me1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

Guo, Y.Nady, N.Qi, C.Allali-Hassani, A.Zhu, H.Pan, P.Adams-Cioaba, M.A.Amaya, M.F.Dong, A.Vedadi, M.Schapira, M.Read, R.J.Arrowsmith, C.H.Min, J.

(2009) Nucleic Acids Res. 37: 2204-2210

  • DOI: 10.1093/nar/gkp086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Ho ...

    The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2-H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl-lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L6, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lethal(3)malignant brain tumor-like 2 protein
A, B
456Homo sapiensMutation(s): 0 
Gene Names: L3MBTL2
Find proteins for Q969R5 (Homo sapiens)
Go to Gene View: L3MBTL2
Go to UniProtKB:  Q969R5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLZ
Query on MLZ

Download SDF File 
Download CCD File 
A, B
N-METHYL-LYSINE
C7 H16 N2 O2
PQNASZJZHFPQLE-LURJTMIESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MLZKd: ~4000000 nM BINDINGMOAD
MLZKd: 14000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.590α = 90.00
b = 55.489β = 90.00
c = 324.101γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description