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PDBsum entry 2c29

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protein ligands links
Oxidoreductase PDB id
2c29
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P93799  (P93799_VITVI) -  Dihydroflavonol 4-reductase
Seq:
Struc:
337 a.a.
324 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.219  - Dihydrokaempferol 4-reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Flavonoid Biosynthesis
      Reaction: Cis-3,4-leucopelargonidin + NADP+ = +-dihydrokaempferol + NADPH
Cis-3,4-leucopelargonidin
Bound ligand (Het Group name = DQH)
matches with 95.00% similarity
+
NADP(+)
Bound ligand (Het Group name = NAP)
corresponds exactly
= (+)-dihydrokaempferol
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extrinsic to endoplasmic reticulum membrane   1 term 
  Biological process     cellular metabolic process   6 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21052759 X.Wang (2011).
Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.
  Funct Integr Genomics, 11, 13-22.  
20386656 H.Halbwirth (2010).
The creation and physiological relevance of divergent hydroxylation patterns in the flavonoid pathway.
  Int J Mol Sci, 11, 595-621.  
20030585 M.Gargouri, J.Chaudière, C.Manigand, C.Maugé, K.Bathany, J.M.Schmitter, and B.Gallois (2010).
The epimerase activity of anthocyanidin reductase from Vitis vinifera and its regiospecific hydride transfers.
  Biol Chem, 391, 219-227.  
20480039 M.Katzberg, N.Skorupa-Parachin, M.F.Gorwa-Grauslund, and M.Bertau (2010).
Engineering cofactor preference of ketone reducing biocatalysts: A mutagenesis study on a gamma-diketone reductase from the yeast Saccharomyces cerevisiae serving as an example.
  Int J Mol Sci, 11, 1735-1758.  
19690377 M.Gargouri, C.Manigand, C.Maugé, T.Granier, B.Langlois d'Estaintot, O.Cala, I.Pianet, K.Bathany, J.Chaudière, and B.Gallois (2009).
Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera.
  Acta Crystallogr D Biol Crystallogr, 65, 989.
PDB codes: 2rh8 3hfs
19588118 Y.Zhang, S.Cheng, D.De Jong, H.Griffiths, R.Halitschke, and W.De Jong (2009).
The potato R locus codes for dihydroflavonol 4-reductase.
  Theor Appl Genet, 119, 931-937.  
18594508 D.L.Des Marais, and M.D.Rausher (2008).
Escape from adaptive conflict after duplication in an anthocyanin pathway gene.
  Nature, 454, 762-765.  
18645237 N.Trabelsi, P.Petit, C.Manigand, B.Langlois d'Estaintot, T.Granier, J.Chaudière, and B.Gallois (2008).
Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols.
  Acta Crystallogr D Biol Crystallogr, (), 883-891.
PDB codes: 3bxx 3c1t
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.