PDBsum entry 1jep

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Isomerase PDB id
Jmol PyMol
Protein chains
212 a.a. *
SO4 ×5
DFL ×2
Waters ×333
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Chalcone isomerase complexed with 4'-hydroxyflavanone
Structure: Chalcone--flavonone isomerase 1. Chain: a, b. Synonym: chalcone isomerase 1. Engineered: yes
Source: Medicago sativa. Organism_taxid: 3879. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
2.10Å     R-factor:   0.206     R-free:   0.232
Authors: J.M.Jez,J.P.Noel
Key ref:
J.M.Jez and J.P.Noel (2002). Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences. J Biol Chem, 277, 1361-1369. PubMed id: 11698411 DOI: 10.1074/jbc.M109224200
18-Jun-01     Release date:   12-Dec-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P28012  (CFI1_MEDSA) -  Chalcone--flavonone isomerase 1
222 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Chalcone isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Flavonoid Biosynthesis
      Reaction: A chalcone = a flavanone
Bound ligand (Het Group name = DFL)
matches with 94.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     flavonoid biosynthetic process   1 term 
  Biochemical function     isomerase activity     3 terms  


    Added reference    
DOI no: 10.1074/jbc.M109224200 J Biol Chem 277:1361-1369 (2002)
PubMed id: 11698411  
Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences.
J.M.Jez, J.P.Noel.
Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of bicyclic chalcones into tricyclic (S)-flavanones. The activity of CHI is essential for the biosynthesis of flavanone precursors of floral pigments and phenylpropanoid plant defense compounds. We have examined the spontaneous and CHI-catalyzed cyclization reactions of 4,2',4',6'-tetrahydroxychalcone, 4,2',4'-trihydroxychalcone, 2',4'-dihydroxychalcone, and 4,2'-dihydroxychalcone into the corresponding flavanones. The pH dependence of flavanone formation indicates that both the non-enzymatic and enzymatic reactions first require the bulk phase ionization of the substrate 2'-hydroxyl group and subsequently on the reactivity of the newly formed 2'-oxyanion during C-ring formation. Solvent viscosity experiments demonstrate that at pH 7.5 the CHI-catalyzed cyclization reactions of 4,2',4',6'-tetrahydroxychalcone, 4,2',4'-trihydroxychalcone, and 2',4'-dihydroxychalcone are approximately 90% diffusion-controlled, whereas cyclization of 4,2'-dihydroxychalcone is limited by a chemical step that likely reflects the higher pK(a) of the 2'-hydroxyl group. At pH 6.0, the reactions with 4,2',4',6'-tetrahydroxychalcone and 4,2',4'-trihydroxychalcone are approximately 50% diffusion-limited, whereas the reactions of both dihydroxychalcones are limited by chemical steps. Comparisons of the 2.1-2.3 A resolution crystal structures of CHI complexed with the products 7,4'-dihydroxyflavanone, 7-hydroxyflavanone, and 4'-hydroxyflavanone show that the 7-hydroxyflavanones all share a common binding mode, whereas 4'-hydroxyflavanone binds in an altered orientation at the active site. Our functional and structural studies support the proposal that CHI accelerates the stereochemically defined intramolecular cyclization of chalcones into biologically active (2S)-flavanones by selectively binding an ionized chalcone in a conformation conducive to ring closure in a diffusion-controlled reaction.
  Selected figure(s)  
Figure 1.
Fig. 1. CHI-catalyzed reaction and active site architecture. A, overall reaction catalyzed by CHI. CHI cyclizes 4,2',4',6'-tetrahydroxychalcone (R[1], R[2], R[3] = OH), 4,2',4'-trihydroxychalcone (R[1], R[3] = OH, R[2] = H), 2',4'-dihydroxychalcone (R[1] = OH, R[2], R[3] = H), and 4,2'-dihydroxychalcone (R[1], R[2] = H, R[3] = OH) into 5,7,4'-trihydroxyflavanone (R[1], R[2], R[3] = OH), 7,4'-dihydroxyflavanone (R[1], R[3] = OH, R[2] = H), 7-hydroxyflavanone (R[1] = OH, R[2], R[3] = H), and 4'-hydroxyflavanone (R[1], R[2] = H, R[3] = OH). The C-ring of the flavanone product is highlighted. B, view of the active site hydrogen bond network in the CHI·naringenin complex (17). Hydrogen bond interactions (small spheres) occur within a network centered on two water molecules (red spheres) that contact the flavanone ketone oxygen and through interactions of the 7-hydroxyl moiety of the flavanone product with Asn113 and Thr190. The figure was prepared with MOLSCRIPT (45) and rendered with POV-Ray (persistence of vision ray tracer; C, proposed cyclization reaction catalyzed by CHI. After nucleophilic attack of the 2'-oxyanion on the , -unsaturated double bond, a water molecule acts as a general acid to stabilize the enolate, resulting in formation of a flav-3-en-4-ol intermediate that tautomerizes into the expected reaction product.
Figure 5.
Fig. 5. Comparison of hydrogen bond interactions in the CHI 7,4'-dihydroxyflavanone (A) and 7-hydroxyflavanone (B) complexes. These views are rotated ~180° around the y axis from the view shown in Fig. 4D and depict the hydrogen bond interactions (dotted lines) at the CHI active site. The figure was prepared with MOLSCRIPT (45) and rendered with POV-Ray (persistence of vision ray-tracer;
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 1361-1369) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22622584 M.N.Ngaki, G.V.Louie, R.N.Philippe, G.Manning, F.Pojer, M.E.Bowman, L.Li, E.Larsen, E.S.Wurtele, and J.P.Noel (2012).
Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis.
  Nature, 485, 530-533.
PDB codes: 4doi 4dok 4dol 4doo
21115265 A.S.Bommarius, J.K.Blum, and M.J.Abrahamson (2011).
Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst.
  Curr Opin Chem Biol, 15, 194-200.  
21052759 X.Wang (2011).
Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.
  Funct Integr Genomics, 11, 13-22.  
20309543 H.Du, Y.Huang, and Y.Tang (2010).
Genetic and metabolic engineering of isoflavonoid biosynthesis.
  Appl Microbiol Biotechnol, 86, 1293-1312.  
20179877 P.Domínguez de María, R.W.van Gemert, A.J.Straathof, and U.Hanefeld (2010).
Biosynthesis of ethers: unusual or common natural events?
  Nat Prod Rep, 27, 370-392.  
19504262 H.C.Zhang, J.M.Liu, H.Y.Lu, and S.L.Gao (2009).
Enhanced flavonoid production in hairy root cultures of Glycyrrhiza uralensis Fisch by combining the over-expression of chalcone isomerase gene with the elicitation treatment.
  Plant Cell Rep, 28, 1205-1213.  
18031469 C.Lillo, U.S.Lea, and P.Ruoff (2008).
Nutrient depletion as a key factor for manipulating gene expression and product formation in different branches of the flavonoid pathway.
  Plant Cell Environ, 31, 587-601.  
18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
  Plant J, 54, 750-762.  
17722151 J.Beekwilder, I.M.van der Meer, O.Sibbesen, M.Broekgaarden, I.Qvist, J.D.Mikkelsen, and R.D.Hall (2007).
Microbial production of natural raspberry ketone.
  Biotechnol J, 2, 1270-1279.  
16960736 Y.Katsuyama, I.Miyahisa, N.Funa, and S.Horinouchi (2007).
One-pot synthesis of genistein from tyrosine by coincubation of genetically engineered Escherichia coli and Saccharomyces cerevisiae cells.
  Appl Microbiol Biotechnol, 73, 1143-1149.  
16575575 C.D.Dana, D.R.Bevan, and B.S.Winkel (2006).
Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure.
  J Mol Model, 12, 905-914.  
14718655 M.Gensheimer, and A.Mushegian (2004).
Chalcone isomerase family and fold: no longer unique to plants.
  Protein Sci, 13, 540-544.  
14978275 S.Hur, Z.E.Newby, and T.C.Bruice (2004).
Transition state stabilization by general acid catalysis, water expulsion, and enzyme reorganization in Medicago savita chalcone isomerase.
  Proc Natl Acad Sci U S A, 101, 2730-2735.  
15503141 S.Kim, R.Jones, K.S.Yoo, and L.M.Pike (2004).
Gold color in onions (Allium cepa): a natural mutation of the chalcone isomerase gene resulting in a premature stop codon.
  Mol Genet Genomics, 272, 411-419.  
11960739 B.Winkel-Shirley (2002).
Biosynthesis of flavonoids and effects of stress.
  Curr Opin Plant Biol, 5, 218-223.  
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.