PDBsum entry 1eyq

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Isomerase PDB id
Protein chains
212 a.a. *
SO4 ×5
NAR ×2
Waters ×382
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Chalcone isomerase and naringenin
Structure: Chalcone-flavonone isomerase 1. Chain: a, b. Synonym: chalcone isomerase 1. Engineered: yes
Source: Medicago sativa. Organism_taxid: 3879. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
1.85Å     R-factor:   0.237     R-free:   0.262
Authors: J.M.Jez,M.E.Bowman,R.A.Dixon,J.P.Noel
Key ref:
J.M.Jez et al. (2000). Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase. Nat Struct Biol, 7, 786-791. PubMed id: 10966651 DOI: 10.1038/79025
08-May-00     Release date:   06-Sep-00    
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 = NAR)
matches with 85.00% 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: 10.1038/79025 Nat Struct Biol 7:786-791 (2000)
PubMed id: 10966651  
Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase.
J.M.Jez, M.E.Bowman, R.A.Dixon, J.P.Noel.
Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcone synthesized by chalcone synthase (CHS) into (2S)-naringenin, an essential compound in the biosynthesis of anthocyanin pigments, inducers of Rhizobium nodulation genes, and antimicrobial phytoalexins. The 1.85 A resolution crystal structure of alfalfa CHI in complex with (2S)-naringenin reveals a novel open-faced beta-sandwich fold. Currently, proteins with homologous primary sequences are found only in higher plants. The topology of the active site cleft defines the stereochemistry of the cyclization reaction. The structure and mutational analysis suggest a mechanism in which shape complementarity of the binding cleft locks the substrate into a constrained conformation that allows the reaction to proceed with a second-order rate constant approaching the diffusion controlled limit. This structure raises questions about the evolutionary history of this structurally unique plant enzyme.
  Selected figure(s)  
Figure 2.
Figure 2. (2S)-Naringenin binding and structure of the active site cleft of CHI. a, Stereo view of the SIGMAA-weighted |2F[o] - F[c]| electron density (1.2 ) for (2S)-naringenin (aqua). b, Stereo view of residues in the active site cleft. (2S)-Naringenin and a water molecule are also shown. Hydrogen bond interactions are indicated with dotted lines (rose). This view is oriented looking into the cleft. c, Stereo view surface representation of the active site cleft showing the fit of (2S)-naringenin and a water molecule. The surface corresponding to Lys 109 and Asn 113 has been removed for clarity.
Figure 4.
Figure 4. Proposed reaction mechanism of CHI. a, View of the active site hydrogen bond network. This view is oriented looking out of the active site cleft. Dotted lines (rose) indicate hydrogen bonds. b, Schematic representation of the active site hydrogen bonds. Distances are indicated in . c, Proposed cyclization reaction catalyzed by CHI. Following nucleophilic attack of the 2'-oxyanion on the , -unsaturated double bond in a Michael addition, the water molecule stabilized by Tyr 106 acts as a general acid to stabilize the enolate. This results in formation of a flav-3-en-4-ol intermediate that tautomerizes into the reaction product. Rendered figures were prepared with MOLSCRIPT40 or GRASP41 and rendered with POV-Ray42.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 786-791) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21338917 A.Rosado, G.R.Hicks, L.Norambuena, I.Rogachev, S.Meir, L.Pourcel, J.Zouhar, M.Q.Brown, M.P.Boirsdore, R.S.Puckrin, S.R.Cutler, E.Rojo, A.Aharoni, and N.V.Raikhel (2011).
Sortin1-hypersensitive mutants link vacuolar-trafficking defects and flavonoid metabolism in Arabidopsis vegetative tissues.
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21046109 H.Cheng, L.Li, S.Cheng, F.Cao, Y.Wang, and H.Yuan (2011).
Molecular cloning and function assay of a chalcone isomerase gene (GbCHI) from Ginkgo biloba.
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21226200 I.Tuñón, and J.T.Hynes (2011).
A simple model for barrier frequencies for enzymatic reactions.
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20805191 M.Wang, Y.Y.Jiang, K.M.Kim, G.Qu, H.F.Ji, J.E.Mittenthal, H.Y.Zhang, and G.Caetano-Anollés (2011).
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation.
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21221632 X.He, J.W.Blount, S.Ge, Y.Tang, and R.A.Dixon (2011).
A genomic approach to isoflavone biosynthesis in kudzu (Pueraria lobata).
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21052759 X.Wang (2011).
Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.
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20179877 P.Domínguez de María, R.W.van Gemert, A.J.Straathof, and U.Hanefeld (2010).
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Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols.
  Acta Crystallogr D Biol Crystallogr, 64, 883-891.
PDB codes: 3bxx 3c1t
18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
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17935117 F.Ververidis, E.Trantas, C.Douglas, G.Vollmer, G.Kretzschmar, and N.Panopoulos (2007).
Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part I: Chemical diversity, impacts on plant biology and human health.
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17701137 J.Lättig, M.Böhl, P.Fischer, S.Tischer, C.Tietböhl, M.Menschikowski, H.O.Gutzeit, P.Metz, and M.T.Pisabarro (2007).
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design.
  J Comput Aided Mol Des, 21, 473-483.  
17806100 Y.Yan, L.Huang, and M.A.Koffas (2007).
Biosynthesis of 5-deoxyflavanones in microorganisms.
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16669781 E.Grotewold (2006).
The genetics and biochemistry of floral pigments.
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16832053 E.Ono, M.Fukuchi-Mizutani, N.Nakamura, Y.Fukui, K.Yonekura-Sakakibara, M.Yamaguchi, T.Nakayama, T.Tanaka, T.Kusumi, and Y.Tanaka (2006).
Yellow flowers generated by expression of the aurone biosynthetic pathway.
  Proc Natl Acad Sci U S A, 103, 11075-11080.  
16367960 E.Ono, M.Hatayama, Y.Isono, T.Sato, R.Watanabe, K.Yonekura-Sakakibara, M.Fukuchi-Mizutani, Y.Tanaka, T.Kusumi, T.Nishino, and T.Nakayama (2006).
Localization of a flavonoid biosynthetic polyphenol oxidase in vacuoles.
  Plant J, 45, 133-143.  
16482434 L.Tian, and R.A.Dixon (2006).
Engineering isoflavone metabolism with an artificial bifunctional enzyme.
  Planta, 224, 496-507.  
15778971 D.G.Covell, A.Wallqvist, R.Huang, N.Thanki, A.A.Rabow, and X.J.Lu (2005).
Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases.
  Proteins, 59, 403-433.  
15770480 I.Miyahisa, M.Kaneko, N.Funa, H.Kawasaki, H.Kojima, Y.Ohnishi, and S.Horinouchi (2005).
Efficient production of (2S)-flavanones by Escherichia coli containing an artificial biosynthetic gene cluster.
  Appl Microbiol Biotechnol, 68, 498-504.  
15952903 S.W.White, J.Zheng, Y.M.Zhang, and Rock (2005).
The structural biology of type II fatty acid biosynthesis.
  Annu Rev Biochem, 74, 791-831.  
15930622 X.Ma, J.Koepke, A.Bayer, G.Fritzsch, H.Michel, and J.Stöckigt (2005).
Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.
  Acta Crystallogr D Biol Crystallogr, 61, 694-696.  
15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
  Annu Rev Plant Biol, 55, 85.  
14570878 J.J.Turnbull, J.Nakajima, R.W.Welford, M.Yamazaki, K.Saito, and C.J.Schofield (2004).
Mechanistic studies on three 2-oxoglutarate-dependent oxygenases of flavonoid biosynthesis: anthocyanidin synthase, flavonol synthase, and flavanone 3beta-hydroxylase.
  J Biol Chem, 279, 1206-1216.  
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.  
15253836 W.Bains (2004).
Many chemistries could be used to build living systems.
  Astrobiology, 4, 137-167.  
12795704 B.Liu, H.Falkenstein-Paul, W.Schmidt, and L.Beerhues (2003).
Benzophenone synthase and chalcone synthase from Hypericum androsaemum cell cultures: cDNA cloning, functional expression, and site-directed mutagenesis of two polyketide synthases.
  Plant J, 34, 847-855.  
12732539 E.I.Hwang, M.Kaneko, Y.Ohnishi, and S.Horinouchi (2003).
Production of plant-specific flavanones by Escherichia coli containing an artificial gene cluster.
  Appl Environ Microbiol, 69, 2699-2706.  
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.