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PDBsum entry 2ybp

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase/peptide PDB id
2ybp
Jmol
Contents
Protein chains
349 a.a.
12 a.a.
Ligands
GOL
2HG ×2
Metals
_NI ×2
_ZN ×2
Waters ×610
PDB id:
2ybp
Name: Oxidoreductase/peptide
Title: Jmjd2a complexed with r-2-hydroxyglutarate and histone h3k36 peptide (30-41)
Structure: Lysine-specific demethylase 4a. Chain: a, b. Fragment: catalytic domain, residues 1-359. Synonym: jmjc domain-containing histone demethylation prote jumonji domain-containing protein 2a. Engineered: yes. Histone h3.1t. Chain: c, d. Fragment: histone h3k36me3 peptide, residues 31-42.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: r3. Synthetic: yes. Organism_taxid: 9606
Resolution:
2.02Å     R-factor:   0.201     R-free:   0.225
Authors: R.Chowdhury,M.A.Mcdonough,C.J.Schofield
Key ref: R.Chowdhury et al. (2011). The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep, 12, 463-469. PubMed id: 21460794
Date:
09-Mar-11     Release date:   30-Mar-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O75164  (KDM4A_HUMAN) -  Lysine-specific demethylase 4A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1064 a.a.
349 a.a.
Protein chains
Pfam   ArchSchema ?
Q16695  (H31T_HUMAN) -  Histone H3.1t
Seq:
Struc:
136 a.a.
12 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
EMBO Rep 12:463-469 (2011)
PubMed id: 21460794  
 
 
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
R.Chowdhury, K.K.Yeoh, Y.M.Tian, L.Hillringhaus, E.A.Bagg, N.R.Rose, I.K.Leung, X.S.Li, E.C.Woon, M.Yang, M.A.McDonough, O.N.King, I.J.Clifton, R.J.Klose, T.D.Claridge, P.J.Ratcliffe, C.J.Schofield, A.Kawamura.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22898539 A.H.Shih, O.Abdel-Wahab, J.P.Patel, and R.L.Levine (2012).
The role of mutations in epigenetic regulators in myeloid malignancies.
  Nat Rev Cancer, 12, 599-612.  
23151579 A.Schulze, and A.L.Harris (2012).
How cancer metabolism is tuned for proliferation and vulnerable to disruption.
  Nature, 491, 364-373.  
22343901 C.Lu, P.S.Ward, G.S.Kapoor, D.Rohle, S.Turcan, O.Abdel-Wahab, C.R.Edwards, R.Khanin, M.E.Figueroa, A.Melnick, K.E.Wellen, D.M.O'Rourke, S.L.Berger, T.A.Chan, R.L.Levine, I.K.Mellinghoff, and C.B.Thompson (2012).
IDH mutation impairs histone demethylation and results in a block to cell differentiation.
  Nature, 483, 474-478.  
23001348 D.C.Wallace (2012).
Mitochondria and cancer.
  Nat Rev Cancer, 12, 685-698.  
22763442 M.Sasaki, C.B.Knobbe, J.C.Munger, E.F.Lind, D.Brenner, A.Brüstle, I.S.Harris, R.Holmes, A.Wakeham, J.Haight, A.You-Ten, W.Y.Li, S.Schalm, S.M.Su, C.Virtanen, G.Reifenberger, P.S.Ohashi, D.L.Barber, M.E.Figueroa, A.Melnick, J.C.Zúñiga-Pflücker, and T.W.Mak (2012).
IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics.
  Nature, 488, 656-659.  
22343896 P.Koivunen, S.Lee, C.G.Duncan, G.Lopez, G.Lu, S.Ramkissoon, J.A.Losman, P.Joensuu, U.Bergmann, S.Gross, J.Travins, S.Weiss, R.Looper, K.L.Ligon, R.G.Verhaak, H.Yan, and W.G.Kaelin (2012).
Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation.
  Nature, 483, 484-488.  
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.