3KVB

Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.

Horton, J.R., Upadhyay, A.K., Qi, H.H., Zhang, X., Shi, Y., Cheng, X.

(2010) Nat Struct Mol Biol 17: 38-43

  • DOI: 10.1038/nsmb.1753
  • Primary Citation of Related Structures:  
    3KV6, 3KV9, 3KV4, 3KV5, 3KVA, 3KVB

  • PubMed Abstract: 

    • Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 ...

    Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
JmjC domain-containing histone demethylation protein 1D A397Homo sapiensMutation(s): 0 
Gene Names: JHDM1D, KIAA1718, KDM7A, KDM7
EC: 2 (PDB Primary Data), 1.14.11 (UniProt)
Find proteins for Q6ZMT4 (Homo sapiens)
Explore Q6ZMT4 
Go to UniProtKB:  Q6ZMT4
NIH Common Fund Data Resources
PHAROS:  Q6ZMT4
GTEx:  ENSG00000006459
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA
Download Ideal Coordinates CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
OXY
Query on OXY
Download Ideal Coordinates CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.3α = 90
b = 78.3β = 90
c = 289.1γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance