3N9L

ceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

Yang, Y.Hu, L.Wang, P.Hou, H.Lin, Y.Liu, Y.Li, Z.Gong, R.Feng, X.Zhou, L.Zhang, W.Dong, Y.Yang, H.Lin, H.Wang, Y.Chen, C.D.Xu, Y.

(2010) Cell Res. 20: 886-898

  • DOI: 10.1038/cr.2010.86
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence- and methylation-state-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently fo ...

    Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence- and methylation-state-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently found that ceKDM7A, a PHD- and JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo. To provide structural insight into the molecular mechanisms for the enzymatic activity and the function of the PHD finger, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures indicate that H3K9me2 and H3K27me2 interact with ceKDM7A in a similar fashion, and that the peptide-binding specificity is determined by a network of specific interactions. The geometrical measurement of the structures also revealed that H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism. Thus, our systemic structural studies reveal not only the substrate recognition by the catalytic domain but also more importantly, the molecular mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.


    Organizational Affiliation

    Cancer Institute, Shanghai Cancer Center, Fudan University, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A
528Caenorhabditis elegansMutation(s): 0 
Gene Names: jmjd-1.2
EC: 1.14.11.-
Find proteins for Q9GYI0 (Caenorhabditis elegans)
Go to UniProtKB:  Q9GYI0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3 peptide
B
15Caenorhabditis elegansMutation(s): 0 
Gene Names: his-2, his-6, his-9, his-13, his-17, his-25, his-27, his-32, his-42, his-45, his-49, his-55, his-59, his-63
Find proteins for P08898 (Caenorhabditis elegans)
Go to UniProtKB:  P08898
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.912α = 90.00
b = 87.264β = 90.00
c = 102.491γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection
PHASESphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance