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PDBsum entry 4ezh
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
4ezh

 

 

 

 

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Contents
Protein chains
455 a.a.
11 a.a.
Ligands
OGA ×2
Metals
_NI ×2
_ZN ×2
Waters ×82
PDB id:
4ezh
Name: Oxidoreductase
Title: The crystal structure of kdm6b bound with h3k27me3 peptide
Structure: Lysine-specific demethylase 6b. Chain: a, b. Fragment: unp residues 1155-1641. Synonym: jmjc domain-containing protein 3, jumonji domain-containing protein 3. Engineered: yes. Synthesized methylation peptide. Chain: c, d. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: kdm6b, jmjd3, kiaa0346. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.
Resolution:
2.52Å     R-factor:   0.215     R-free:   0.254
Authors: Z.J.Cheng,D.J.Patel
Key ref: L.Kruidenier et al. (2012). A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature, 488, 404-408. PubMed id: 22842901
Date:
02-May-12     Release date:   08-Aug-12    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5NCY0  (KDM6B_MOUSE) -  Lysine-specific demethylase 6B from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1641 a.a.
455 a.a.*
Protein chains
Pfam   ArchSchema ?
P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens
Seq:
Struc: 		136 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.14.11.68  - [histone H3]-trimethyl-L-lysine(27) demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl27-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
N(6),N(6),N(6)-trimethyl-L-lysyl(27)-[histone H3]
 + 2 × 2-oxoglutarate
 + 2 × O2
 = N(6)-methyl-L-lysyl(27)-[histone H3]
 + 2 × formaldehyde
 + 2 × succinate
 + 2 × CO2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nature 488:404-408 (2012)
PubMed id: 22842901  
 
 
A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.
L.Kruidenier, C.W.Chung, Z.Cheng, J.Liddle, K.Che, G.Joberty, M.Bantscheff, C.Bountra, A.Bridges, H.Diallo, D.Eberhard, S.Hutchinson, E.Jones, R.Katso, M.Leveridge, P.K.Mander, J.Mosley, C.Ramirez-Molina, P.Rowland, C.J.Schofield, R.J.Sheppard, J.E.Smith, C.Swales, R.Tanner, P.Thomas, A.Tumber, G.Drewes, U.Oppermann, D.J.Patel, K.Lee, D.M.Wilson.
 
  ABSTRACT  
 
No abstract given.

 

 

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