PDBsum entry 2c29

Oxidoreductase

PDB id: 2c29

Contents

Protein chains

324 a.a. *

Ligands

NAP ×2

DQH ×2

Waters ×576

* Residue conservation analysis

PDB id:

2c29

Name:

Oxidoreductase

Title:

Structure of dihydroflavonol reductase from vitis vinifera at 1.8 a.

Structure:

Dihydroflavonol 4-reductase. Chain: d, f. Engineered: yes. Other_details: rossmann fold

Source:

Vitis vinifera. Grape. Organism_taxid: 29760. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.81Å R-factor: 0.195 R-free: 0.244

Authors:

P.Petit,T.Granier,B.L.D'Estaintot,S.Hamdi,B.Gallois

Key ref:

P.Petit et al. (2007). Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis. J Mol Biol, 368, 1345-1357. PubMed id: 17395203 DOI: 10.1016/j.jmb.2007.02.088

Date:

27-Sep-05 Release date: 16-Oct-06

Protein chains

P93799  (P93799_VITVI) -  Flavanone 4-reductase from Vitis vinifera

Seq: 337 a.a.

Struc: 324 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.1.1.219 - dihydroflavanol 4-reductase.
• Pathway: Flavonoid Biosynthesis
• Reaction: a (2R,3S,4S)-leucoanthocyanidin + NADP⁺ = a (2R,3R)-dihydroflavonol + NADPH + H⁺

(2R,3S,4S)-leucoanthocyanidin + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = (2R,3R)-dihydroflavonol + NADPH + H(+)

• Enzyme class 2: E.C.1.1.1.234 - flavanone 4-reductase.

Pathway:

• Reaction: (2S)-flavan-4-ol + NADP⁺ = (2S)-flavanone + NADPH + H⁺

(2S)-flavan-4-ol (Bound ligand (Het Group name = DQH) matches with 77.27% similarity) + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = (2S)-flavanone + NADPH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.jmb.2007.02.088

J Mol Biol 368:1345-1357 (2007)

PubMed id: 17395203

Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis.

P.Petit, T.Granier, B.L.d'Estaintot, C.Manigand, K.Bathany, J.M.Schmitter, V.Lauvergeat, S.Hamdi, B.Gallois.

ABSTRACT

The nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enzyme dihydroflavonol 4-reductase (DFR) catalyzes a late step in the biosynthesis of anthocyanins and condensed tannins, two flavonoid classes of importance to plant survival and human nutrition. This enzyme has been widely investigated in many plant species, but little is known about its structural and biochemical properties. To provide a basis for detailed structure-function studies, the crystal structure of Vitis vinifera DFR, heterologously expressed in Escherichia coli, has been determined at 1.8 A resolution. The 3D structure of the ternary complex obtained with the oxidized form of nicotinamide adenine dinucleotide phosphate and dihydroquercetin, one of the DFR substrates, presents common features with the short-chain dehydrogenase/reductase family, i.e., an N-terminal domain adopting a Rossmann fold and a variable C-terminal domain, which participates in substrate binding. The structure confirms the importance of the 131-156 region, which lines the substrate binding site and enlightens the role of a specific residue at position 133 (Asn or Asp), assumed to control substrate recognition. The activity of the wild-type enzyme and its variant N133D has been quantified in vitro, using dihydroquercetin or dihydrokaempferol. Our results demonstrate that position 133 cannot be solely responsible for the recognition of the B-ring hydroxylation pattern of dihydroflavonols.

Selected figure(s)

Figure 1.
Figure 1. Final steps of the flavonoid biosynthetic pathway leading to the synthesis of anthocyanins and condensed tannins (proanthocyanidins). DFR, dihydroflavonol 4-reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; LAR, leucoanthocyanidin reductase; UFGT, 3-O-glycosyltransferase. Figure 1. Final steps of the flavonoid biosynthetic pathway leading to the synthesis of anthocyanins and condensed tannins (proanthocyanidins). DFR, dihydroflavonol 4-reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; LAR, leucoanthocyanidin reductase; UFGT, 3-O-glycosyltransferase.

Figure 5.
Figure 5. (a) Geometry of the catalytic triad site. (b) Stereo view of the catalytic site in the vicinity of the K167 side-chain. The lysine amino group interacts with a cluster of five water molecules filling a hydrophilic cavity. (c) Stereo view of the substrate binding site. DHQ is wrapped up by the N and C-terminal parts of the protein: contacts are established via hydrophilic interactions or hydrophobic residues of both N and C-terminal domains. The color code is the same as in the legend to Figure 4. Figure 5. (a) Geometry of the catalytic triad site. (b) Stereo view of the catalytic site in the vicinity of the K167 side-chain. The lysine amino group interacts with a cluster of five water molecules filling a hydrophilic cavity. (c) Stereo view of the substrate binding site. DHQ is wrapped up by the N and C-terminal parts of the protein: contacts are established via hydrophilic interactions or hydrophobic residues of both N and C-terminal domains. The color code is the same as in the legend to [3]Figure 4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 1345-1357) copyright 2007.

Figures were selected by an automated process.