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PDBsum entry 3avr
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase/structural protein PDB id
3avr

 

 

 

 

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Contents
Protein chains
473 a.a.
17 a.a.
Ligands
OGA
EDO ×9
Metals
_CL ×2
_ZN
_NI
Waters ×388
PDB id:
3avr
Name: Oxidoreductase/structural protein
Title: Catalytic fragment of utx/kdm6a bound with histone h3k27me3 peptide, n-oxyalylglycine, and ni(ii)
Structure: Lysine-specific demethylase 6a. Chain: a. Fragment: unp residues 880-1401. Synonym: histone demethylase utx, ubiquitously-transcribed tpr protein on the x chromosome, ubiquitously-transcribed x chromosome tetratricopeptide repeat protein. Engineered: yes. Histone h3. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm6a, utx. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemical synthesis
Resolution:
1.80Å     R-factor:   0.171     R-free:   0.198
Authors: T.Sengoku,S.Yokoyama
Key ref: T.Sengoku and S.Yokoyama (2011). Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. Genes Dev, 25, 2266-2277. PubMed id: 22002947
Date:
07-Mar-11     Release date:   19-Oct-11    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
O15550  (KDM6A_HUMAN) -  Lysine-specific demethylase 6A from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1401 a.a.
473 a.a.
Protein chain
Pfam   ArchSchema ?
P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens
Seq:
Struc: 		136 a.a.
17 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: 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
Bound ligand (Het Group name = EDO)
matches with 50.00% similarity 		+ 2 × succinate
 + 2 × CO2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Genes Dev 25:2266-2277 (2011)
PubMed id: 22002947  
 
 
Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A.
T.Sengoku, S.Yokoyama.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22842901 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, and D.M.Wilson (2012).
A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.
  Nature, 488, 404-408.
PDB codes: 2xue 4ask 4eyu 4ez4 4ezh
23175120 P.A.Northcott, D.T.Jones, M.Kool, G.W.Robinson, R.J.Gilbertson, Y.J.Cho, S.L.Pomeroy, A.Korshunov, P.Lichter, M.D.Taylor, and S.M.Pfister (2012).
Medulloblastomics: the end of the beginning.
  Nat Rev Cancer, 12, 818-834.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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