PDBsum entry 2zk5

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Transcription PDB id
Protein chain
274 a.a. *
NRO ×2
Waters ×72
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed with nitro-233
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
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pparg. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.45Å     R-factor:   0.245     R-free:   0.306
Authors: T.Waku,T.Shiraki,T.Oyama,Y.Fujimoto,K.Morikawa
Key ref:
T.Waku et al. (2009). Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids. J Mol Biol, 385, 188-199. PubMed id: 18977231 DOI: 10.1016/j.jmb.2008.10.039
12-Mar-08     Release date:   24-Feb-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

 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.jmb.2008.10.039 J Mol Biol 385:188-199 (2009)
PubMed id: 18977231  
Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids.
T.Waku, T.Shiraki, T.Oyama, Y.Fujimoto, K.Maebara, N.Kamiya, H.Jingami, K.Morikawa.
Peroxisome proliferator-activated receptor (PPAR) gamma is a nuclear receptor that regulates lipid homeostasis, and several fatty acid metabolites have been identified as PPARgamma ligands. Here, we present four crystal structures of the PPARgamma ligand binding domain (LBD) covalently bound to endogenous fatty acids via a unique cysteine, which is reportedly critical for receptor activation. The structure analyses of the LBD complexed with 15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) revealed that the covalent binding of 15d-PGJ(2) induced conformational changes in the loop region following helix H2', and rearrangements of the side-chain network around the created covalent bond in the LBD. Point mutations of these repositioned residues on the loop and helix H3 almost completely abolished PPARgamma activation by 15d-PGJ(2), indicating that the observed structural alteration may be crucial for PPARgamma activation by the endogenous fatty acid. To address the issue of partial agonism of endogenous PPARgamma ligands, we took advantage of a series of oxidized eicosatetraenoic acids (oxoETEs) as covalently bound ligands to PPARgamma. Despite similar structural and chemical properties, these fatty acids exhibited distinct degrees of transcriptional activity. Crystallographic studies, using two of the oxoETE/PPARgamma LBD complexes, revealed that transcriptional strength of each oxoETE is associated with the difference in the loop conformation, rather than the interaction between each ligand and helix H12. These results suggest that the loop conformation may be responsible for the modulation of PPARgamma activity. Based on these results, we identified novel agonists covalently bound to PPARgamma by in silico screening and a cell-based assay. Our crystallographic study of LBD complexed with nitro-233 demonstrated that the expected covalent bond is indeed formed between this newly identified agonist and the cysteine. This study presents the structural basis for the activation and modulation mechanism of PPARgamma through covalent modification with endogenous fatty acids.
  Selected figure(s)  
Figure 1.
Fig. 1. Crystal structures of the PPARγ LBD complexed with 15d-PGJ[2]. (a) Overall structures of the apo PPARγ LBD (left-hand panel), and the locked 15d-PGJ[2]/PPARγ LBD (right-hand panel). The C^α atoms of the PPARγ LBDs are depicted as ribbon models in gray (the apo PPARγ LBD), and red (the 15d-PGJ[2]/PPARγ LBD). The fatty acid is depicted as a space-filling model, with carbon and oxygen in gray and red, respectively. (b) Stereo view of the composite omit 2F[o] – F[c] electron density map (contoured at 1σ) for 15d-PGJ[2] and Cys285. The fatty acid and the cysteine residue are also represented as stick models. (c) A representation of the interaction between PPARγ and 15d-PGJ[2], which is shown as black lines. Hydrophobic interactions are indicated by broken lines, and hydrogen bonds are denoted by arrows from proton donors to acceptors. Broken arrows indicate weak hydrogen bonds, such as CH-donor and pi-acceptor hydrogen bonds. The covalent bond between the fatty acid and Cys285 is marked by a red line. The chiral conformation around the carbon atom covalently bound to Cys285 is (S).
Figure 4.
Fig. 4. Crystal structures of PPARγ LBDs complexed with oxoETEs. (a) Close-up views of the bound 8-oxoETE (green, left-hand panel) and 15-oxoETE (orange, right-hand panel). The side chains of Cys285 and Tyr473 in both structures are depicted as stick models, and each oxoETE is shown as a space-filling model, with carbon, oxygen, and nitrogen in gray, red, and blue, respectively. (b) The composite omit 2F[o] – F[c] electron density maps (contoured at 1σ) for 8-oxoETE (left-hand panel) and 15-oxoETE (right-hand panels). The covalent binding between Cys285 and oxoETE is also represented as stick models. A water molecule is shown as a red sphere. (c) Superposition of 15d-PGJ[2] (red), 8-oxoETE (green), and 15-oxoETE (orange). (d) The side-chain orientation around Cys285 on the helix H3. The side chains of the residues around Cys285 on the helix H3 among the PPARγ LBDs complexed with 15d-PGJ[2], 8-oxoETE, and 15-oxoETE are depicted as stick models in red, green, and orange, respectively. The C^α atoms of all structures are depicted as gray ribbon models, except for omitted fatty acids. (e) Structural comparison of the loop between helix H2′ and helix H3. The C^α atoms of the PPARγ LBDs complexed with 15d-PGJ[2], 8-oxoETE, and 15-oxoETE are depicted as ribbon models in red, green, and orange, respectively.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 188-199) copyright 2009.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482446 B.O.Al-Najjar, H.A.Wahab, T.S.Tengku Muhammad, A.C.Shu-Chien, N.A.Ahmad Noruddin, and M.O.Taha (2011).
Discovery of new nanomolar peroxisome proliferator-activated receptor γ activators via elaborate ligand-based modeling.
  Eur J Med Chem, 46, 2513-2529.  
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.  
20673203 A.N.Smirnov (2010).
Lipid signaling in the atherogenesis context.
  Biochemistry (Mosc), 75, 793-810.  
20689419 F.Grün (2010).
  Curr Opin Endocrinol Diabetes Obes, 17, 453-459.  
20231490 L.M.Koharudin, H.Liu, R.Di Maio, R.B.Kodali, S.H.Graham, and A.M.Gronenborn (2010).
Cyclopentenone prostaglandin-induced unfolding and aggregation of the Parkinson disease-associated UCH-L1.
  Proc Natl Acad Sci U S A, 107, 6835-6840.  
19746174 S.N.Lewis, J.Bassaganya-Riera, and D.R.Bevan (2010).
Virtual Screening as a Technique for PPAR Modulator Discovery.
  PPAR Res, 2010, 861238.  
20717101 T.Waku, T.Shiraki, T.Oyama, K.Maebara, R.Nakamori, and K.Morikawa (2010).
The nuclear receptor PPARγ individually responds to serotonin- and fatty acid-metabolites.
  EMBO J, 29, 3395-3407.
PDB codes: 2zk6 3ads 3adt 3adu 3adv 3adw 3adx
19996102 Y.Fujimoto, T.Shiraki, Y.Horiuchi, T.Waku, A.Shigenaga, A.Otaka, T.Ikura, K.Igarashi, S.Aimoto, S.Tate, and K.Morikawa (2010).
Proline cis/trans-isomerase Pin1 regulates peroxisome proliferator-activated receptor gamma activity through the direct binding to the activation function-1 domain.
  J Biol Chem, 285, 3126-3132.  
19748282 E.H.Jeninga, M.Gurnell, and E.Kalkhoven (2009).
Functional implications of genetic variation in human PPARgamma.
  Trends Endocrinol Metab, 20, 380-387.  
19622862 T.Oyama, K.Toyota, T.Waku, Y.Hirakawa, N.Nagasawa, J.I.Kasuga, Y.Hashimoto, H.Miyachi, and K.Morikawa (2009).
Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures.
  Acta Crystallogr D Biol Crystallogr, 65, 786-795.
PDB codes: 2znn 2zno 2znp 2znq
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