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PDBsum entry 2yu1

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protein ligands metals links
Oxidoreductase PDB id
2yu1
Jmol
Contents
Protein chain
386 a.a. *
Ligands
AKG
Metals
FE2
Waters ×74
* Residue conservation analysis
PDB id:
2yu1
Name: Oxidoreductase
Title: Crystal structure of hjhdm1a complexed with a-ketoglutarate
Structure: Jmjc domain-containing histone demethylation prot chain: a. Fragment: residues 1-383, residues 450-517. Synonym: [histone-h3]-lysine-36 demethylase 1a, f-box/lrr- protein 11, f-box and leucine-rich repeat protein 11, f-box fbl7, f-box protein lilina. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hjhdm1a. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.70Å     R-factor:   0.238     R-free:   0.273
Authors: Z.Han
Key ref: Z.Han et al. Structural basis for histone demethylation by jhdm1. To be published, .
Date:
05-Apr-07     Release date:   24-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y2K7  (KDM2A_HUMAN) -  Lysine-specific demethylase 2A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1162 a.a.
386 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.27  - [Histone H3]-lysine-36 demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Protein N6,N6-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N6-methyl-L-lysine + succinate + formaldehyde + CO2
2. Protein N6-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2
Protein N(6),N(6)-dimethyl-L-lysine
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ O(2)
= protein N(6)-methyl-L-lysine
+ succinate
+ formaldehyde
+ CO(2)
Protein N(6)-methyl-L-lysine
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ O(2)
= protein L-lysine
+ succinate
+ formaldehyde
+ CO(2)
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site