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Catalytic Site Atlas

CSA LITERATURE entry for 1eyp

E.C. namechalcone isomerase
SpeciesMedicago sativa (Alfalfa)
E.C. Number (IntEnz)
CSA Homologues of 1eyp1eyq,1fm7,1fm8,1jep,1jx0,1jx1,
CSA Entries With UniProtID P28012
CSA Entries With EC Number
PDBe Entry 1eyp
PDBSum Entry 1eyp
MACiE Entry M0196

Literature Report

IntroductionChalcone isomerase is required in plant flavonoid biosynthesis, catalysing the cyclisation of chalcone with a 1:100,000 preference for the S-isomer over the R- isomer. This pathway is well characterised, and so the flavonoid biosynthetic enzymes are attractive targets for metabolic engineering.
MechansimThe overall mechanism is a Michael addition; the intra-molecular nucleophilic attack of a hydroxyl at a carbonyl in the chalcone substrate, through a six member transition state to form (2S)-naringenin. Modelling studies implicate an electron flow towards the C alpha atom, forming a corresponding carbanion transition state. The charge on this carbon atom increases substantially more than the charge found on the carbonyl oxygen atom. The proximity of the C alpha to a positively charged lysine, and the resulting stabilisation is thought to be the largest contribution to the enzyme's catalytic power. This Lys is thought to then act as a general acid to the anionic transition state through a water molecule.
The ability of the active site to accommodate and stabilise the charge distribution of the transition state drives catalysis.

Catalytic Sites for 1eyp

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA9797macie:sideChainThe positively charged residue polarises a close proximity water molecule, which then acts to stabilise the carbanionic transition state. The electrostatic potential is important in lowering the energy of the transition state relative to the reactant. The residue is also necessary to induce protonation of the anion by the water molecule through hydrogen bond interactions.
ThrA4848macie:sideChainThe residue hydroxyl interacts with the O7 of the substrate (the carbonyl oxygen), and orientates the transition state towards the Lys 97 residue. Mutation of Thr 48 to Ala results in a loss of catalytic function by roughly 1000 fold.
TyrA106106macie:sideChain The residue establishes a hydrogen bond with the 6' hydroxyl group of the substrate through a water molecule. This interaction is significantly stronger in the transition state than in the reactant state, making a favourable interaction to lower the free energy barrier.

Literature References

Ruiz-PernĂ­a JJ
Enzymatic effects on reactant and transition states. The case of chalcone isomerase.
J Am Chem Soc 2007 129 9117-9124
PubMed: 17602559
Hur S
Transition state stabilization by general acid catalysis, water expulsion, and enzyme reorganization in Medicago savita chalcone isomerase.
Proc Natl Acad Sci U S A 2004 101 2730-2735
PubMed: 14978275
Jez JM
Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase.
Nat Struct Biol 2000 7 786-791
PubMed: 10966651