PDBsum entry 4idf

Oxidoreductase

PDB id: 4idf

Contents

Protein chain

321 a.a.

Ligands

NDP

4XX

SO4

EDO ×2

Waters ×502

PDB id:

4idf

Name:

Oxidoreductase

Title:

Structure of the fragaria x ananassa enone oxidoreductase in complex with NADPH and hmf

Structure:

Ripening-induced protein. Chain: a. Fragment: unp residues 17-336. Synonym: faeo. Engineered: yes

Source:

Fragaria vesca. Woodland strawberry. Organism_taxid: 57918. Gene: gene28406. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.142 R-free: 0.163

Authors:

A.Schiefner,A.Skerra

Key ref:

A.Schiefner et al. (2013). Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone. J Biol Chem, 288, 16815-16826. PubMed id: 23589283 DOI: 10.1074/jbc.M113.453852

Date:

12-Dec-12 Release date: 17-Apr-13

Protein chain

O23939  (ENOX_FRAVE) -  2-methylene-furan-3-one reductase from Fragaria vesca

Seq: 322 a.a.

Struc: 321 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.3.1.105 - 2-methylene-furan-3-one reductase.
• Reaction: 4-hydroxy-2,5-dimethyl-furan-3(2H)-one + NADP⁺ = 4-hydroxy-5-methyl-2- methylenefuran-3(2H)-one + NADPH + H⁺

4-hydroxy-2,5-dimethyl-furan-3(2H)-one + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 4-hydroxy-5-methyl-2- methylenefuran-3(2H)-one + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M113.453852

J Biol Chem 288:16815-16826 (2013)

PubMed id: 23589283

Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone.

A.Schiefner, Q.Sinz, I.Neumaier, W.Schwab, A.Skerra.

ABSTRACT

The last step in the biosynthetic route to the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) is catalyzed by Fragaria x ananassa enone oxidoreductase (FaEO), earlier putatively assigned as quinone oxidoreductase (FaQR). The ripening-induced enzyme catalyzes the reduction of the exocyclic double bond of the highly reactive precursor 4-hydroxy-5-methyl-2-methylene-3(2H)-furanone (HMMF) in a NAD(P)H-dependent manner. To elucidate the molecular mechanism of this peculiar reaction, we determined the crystal structure of FaEO in six different states or complexes at resolutions of ≤1.6 Å, including those with HDMF as well as three distinct substrate analogs. Our crystallographic analysis revealed a monomeric enzyme whose active site is largely determined by the bound NAD(P)H cofactor, which is embedded in a Rossmann-fold. Considering that the quasi-symmetric enolic reaction product HDMF is prone to extensive tautomerization, whereas its precursor HMMF is chemically labile in aqueous solution, we used the asymmetric and more stable surrogate product 2-ethyl-4-hydroxy-5-methyl-3(2H)-furanone (EHMF) and the corresponding substrate (2E)-ethylidene-4-hydroxy-5-methyl-3(2H)-furanone (EDHMF) to study their enzyme complexes as well. Together with deuterium-labeling experiments of EDHMF reduction by [4R-(2)H]NADH and chiral-phase analysis of the reaction product EHMF, our data show that the 4R-hydride of NAD(P)H is transferred to the unsaturated exocyclic C6 carbon of HMMF, resulting in a cyclic achiral enolate intermediate that subsequently becomes protonated, eventually leading to HDMF. Apart from elucidating this important reaction of the plant secondary metabolism our study provides a foundation for protein engineering of enone oxidoreductases and their application in biocatalytic processes.