PDBsum entry 2zvt

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protein ligands Protein-protein interface(s) links
Transcription PDB id
Protein chain
274 a.a. *
PTG ×2
Waters ×184
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Cys285ser mutant ppargamma ligand-binding domain complexed with 15-deoxy-delta12,14-prostaglandin j2
Structure: Peroxisome proliferator-activated receptor gamma. Chain: a, b. Fragment: ligand-binding domain. Synonym: ppar-gamma, nuclear receptor subfamily 1 group c member 3. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pparg. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.90Å     R-factor:   0.251     R-free:   0.275
Authors: T.Waku,T.Oyama,T.Shiraki,K.Morikawa
Key ref: T.Waku et al. (2009). Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands. FEBS Lett, 583, 320-324. PubMed id: 19101554 DOI: 10.1016/j.febslet.2008.12.017
19-Nov-08     Release date:   06-Oct-09    
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Protein chains
Pfam   ArchSchema ?
P37231  (PPARG_HUMAN) -  Peroxisome proliferator-activated receptor gamma
505 a.a.
274 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   2 terms 
  Biochemical function     DNA binding     4 terms  


DOI no: 10.1016/j.febslet.2008.12.017 FEBS Lett 583:320-324 (2009)
PubMed id: 19101554  
Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands.
T.Waku, T.Shiraki, T.Oyama, K.Morikawa.
15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) activates a nuclear receptor heterodimer, peroxisome proliferators-activated receptor gamma (PPARgamma)/ retinoid X receptor (RXRalpha) through covalent binding to Cys285 in PPARgamma ligand-binding domain (LBD). Here, we present the 1.9A crystal structure of C285S mutant LBD complexed with 15d-PGJ(2), corresponding to the non-covalently bound state. The ligand lies adjacent to a hydrogen-bond network around the helix H2 and the nearby beta-sheet. Comparisons with previous structures clarified the relationships between PPARgamma function and conformational alterations of LBD during the process of covalently binding ligands, such as 15d-PGJ(2), and thus suggested a mechanism, by which these ligands modulate PPARgamma/RXRalpha function through conformational changes of the loop following helix H2' and the beta-sheet.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21216727 C.Shionyu-Mitsuyama, T.Waku, T.Shiraki, T.Oyama, T.Shirai, and K.Morikawa (2011).
Detecting structural similarity of ligand interactions in the lipid metabolic system including enzymes, lipid-binding proteins and nuclear receptors.
  Protein Eng Des Sel, 24, 397-403.  
20436486 A.L.Groeger, C.Cipollina, M.P.Cole, S.R.Woodcock, G.Bonacci, T.K.Rudolph, V.Rudolph, B.A.Freeman, and F.J.Schopfer (2010).
Cyclooxygenase-2 generates anti-inflammatory mediators from omega-3 fatty acids.
  Nat Chem Biol, 6, 433-441.  
20673203 A.N.Smirnov (2010).
Lipid signaling in the atherogenesis context.
  Biochemistry (Mosc), 75, 793-810.  
20717101 T.Waku, T.Shiraki, T.Oyama, K.Maebara, R.Nakamori, and K.Morikawa (2010).
The nuclear receptor PPARĪ³ individually responds to serotonin- and fatty acid-metabolites.
  EMBO J, 29, 3395-3407.
PDB codes: 2zk6 3ads 3adt 3adu 3adv 3adw 3adx
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