PDBsum entry 1jx0

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Isomerase PDB id
Jmol PyMol
Protein chains
217 a.a. *
205 a.a. *
SO4 ×4
Waters ×101
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Chalcone isomerase--y106f mutant
Structure: Chalcone--flavonone isomerase 1. Chain: a, b. Synonym: chalcone isomerase 1. Engineered: yes. Mutation: yes
Source: Medicago sativa. Organism_taxid: 3879. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.85Å     R-factor:   0.274     R-free:   0.299
Authors: J.M.Jez,M.E.Bowman,J.P.Noel
Key ref:
J.M.Jez et al. (2002). Role of hydrogen bonds in the reaction mechanism of chalcone isomerase. Biochemistry, 41, 5168-5176. PubMed id: 11955065 DOI: 10.1021/bi0255266
05-Sep-01     Release date:   24-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P28012  (CFI1_MEDSA) -  Chalcone--flavonone isomerase 1
222 a.a.
217 a.a.*
Protein chain
Pfam   ArchSchema ?
P28012  (CFI1_MEDSA) -  Chalcone--flavonone isomerase 1
222 a.a.
205 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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

Flavonoid Biosynthesis
      Reaction: A chalcone = a flavanone
Bound ligand (Het Group name = DFV)
matches with 89.00% 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: 10.1021/bi0255266 Biochemistry 41:5168-5176 (2002)
PubMed id: 11955065  
Role of hydrogen bonds in the reaction mechanism of chalcone isomerase.
J.M.Jez, M.E.Bowman, J.P.Noel.
In flavonoid, isoflavonoid, and anthocyanin biosynthesis, chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into (S)-flavanones with a second-order rate constant that approaches the diffusion-controlled limit. The three-dimensional structures of alfalfa CHI complexed with different flavanones indicate that two sets of hydrogen bonds may possess critical roles in catalysis. The first set of interactions includes two conserved amino acids (Thr48 and Tyr106) that mediate a hydrogen bond network with two active site water molecules. The second set of hydrogen bonds occurs between the flavanone 7-hydroxyl group and two active site residues (Asn113 and Thr190). Comparison of the steady-state kinetic parameters of wild-type and mutant CHIs demonstrates that efficient cyclization of various chalcones into their respective flavanones requires both sets of contacts. For example, the T48A, T48S, Y106F, N113A, and T190A mutants exhibit 1550-, 3-, 30-, 7-, and 6-fold reductions in k(cat) and 2-3-fold changes in K(m) with 4,2',4'-trihydroxychalcone as a substrate. Kinetic comparisons of the pH-dependence of the reactions catalyzed by wild-type and mutant enzymes indicate that the active site hydrogen bonds contributed by these four residues do not significantly alter the pK(a) of the intramolecular cyclization reaction. Determinations of solvent kinetic isotope and solvent viscosity effects for wild-type and mutant enzymes reveal a change from a diffusion-controlled reaction to one limited by chemistry in the T48A and Y106F mutants. The X-ray crystal structures of the T48A and Y106F mutants support the assertion that the observed kinetic effects result from the loss of key hydrogen bonds at the CHI active site. Our results are consistent with a reaction mechanism for CHI in which Thr48 polarizes the ketone of the substrate and Tyr106 stabilizes a key catalytic water molecule. Hydrogen bonds contributed by Asn113 and Thr190 provide additional stabilization in the transition state. Conservation of these residues in CHIs from other plant species implies a common reaction mechanism for enzyme-catalyzed flavanone formation in all plants.

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
20309543 H.Du, Y.Huang, and Y.Tang (2010).
Genetic and metabolic engineering of isoflavonoid biosynthesis.
  Appl Microbiol Biotechnol, 86, 1293-1312.  
18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
  Plant J, 54, 750-762.  
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.  
15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
  Annu Rev Plant Biol, 55, 85.  
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.  
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.