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(-) Description

Title :  STRUCTURE OF DIHYDROFLAVONOL REDUCTASE FROM VITIS VINIFERA AT 1.8 A.
 
Authors :  P. Petit, T. Granier, B. L. D'Estaintot, S. Hamdi, B. Gallois
Date :  27 Sep 05  (Deposition) - 16 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  D,F
Biol. Unit 1:  D  (1x)
Biol. Unit 2:  F  (1x)
Keywords :  Flavonoids, Short Dehydrogenase Reductase, Nadph, Dihydroquercetin, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Petit, T. Granier, B. L. D'Estaintot, C. Manigand, K. Bathany, J. M. Schmitter, V. Lauvergeat, S. Hamdi, B. Gallois
Crystal Structure Of Grape Dihydroflavonol 4- Reductase, A Key Enzyme In Flavonoid Biosynthesis.
J. Mol. Biol. V. 368 1345 2007
PubMed-ID: 17395203  |  Reference-DOI: 10.1016/J.JMB.2007.02.088

(-) Compounds

Molecule 1 - DIHYDROFLAVONOL 4-REDUCTASE
    Chains: D, F
    EC Number: 1.1.1.219
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE(30XA)
    Expression System Strain: M15(PREP4)
    Expression System Taxid: 562
    Organism Common: GRAPE
    Organism Scientific: VITIS VINIFERA
    Organism Taxid: 29760
    Other Details: ROSSMANN FOLD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : DF
Biological Unit 1 (1x): D 
Biological Unit 2 (1x):  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DQH2Ligand/Ion(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DQH1Ligand/Ion(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DQH1Ligand/Ion(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER D:14 , GLY D:15 , PHE D:16 , ILE D:17 , VAL D:36 , ARG D:37 , LYS D:44 , ASP D:64 , LEU D:65 , VAL D:84 , ALA D:85 , THR D:86 , MET D:88 , THR D:126 , SER D:127 , TYR D:163 , LYS D:167 , PRO D:190 , THR D:191 , VAL D:193 , PRO D:204 , SER D:205 , DQH D:1331 , HOH D:2003 , HOH D:2032 , HOH D:2042 , HOH D:2081 , HOH D:2256 , HOH D:2257 , HOH D:2258 , HOH D:2259 , HOH D:2260 , HOH D:2261 , HOH D:2264BINDING SITE FOR RESIDUE NAP D1330
2AC2SOFTWARESER D:128 , ALA D:129 , ASN D:133 , ILE D:134 , TYR D:163 , PRO D:190 , THR D:191 , LEU D:192 , PRO D:204 , SER D:205 , THR D:208 , ILE D:222 , GLN D:227 , NAP D:1330 , HOH D:2173 , HOH D:2181 , HOH D:2263 , HOH D:2264BINDING SITE FOR RESIDUE DQH D1331
3AC3SOFTWARESER F:14 , GLY F:15 , PHE F:16 , ILE F:17 , ARG F:37 , LYS F:44 , ASP F:64 , LEU F:65 , VAL F:84 , ALA F:85 , THR F:86 , PRO F:87 , MET F:88 , THR F:126 , SER F:127 , TYR F:163 , LYS F:167 , PRO F:190 , THR F:191 , LEU F:192 , VAL F:193 , PRO F:204 , SER F:205 , DQH F:1332 , HOH F:2006 , HOH F:2010 , HOH F:2093 , HOH F:2304 , HOH F:2306 , HOH F:2307 , HOH F:2308 , HOH F:2309 , HOH F:2310 , HOH F:2311BINDING SITE FOR RESIDUE NAP F1331
4AC4SOFTWARESER F:128 , ALA F:129 , ASN F:133 , ILE F:134 , TYR F:163 , PRO F:190 , THR F:191 , LEU F:192 , PRO F:204 , SER F:205 , THR F:208 , ILE F:222 , GLN F:227 , NAP F:1331 , HOH F:2201 , HOH F:2215 , HOH F:2311 , HOH F:2312BINDING SITE FOR RESIDUE DQH F1332

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C29)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C29)

(-) Exons   (0, 0)

(no "Exon" information available for 2C29)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain D from PDB  Type:PROTEIN  Length:324
 aligned with P93799_VITVI | P93799 from UniProtKB/TrEMBL  Length:337

    Alignment length:324
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
         P93799_VITVI     6 ETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPTNVKKVKHLLDLPKAETHLTLWKADLADEGSFDEAIKGCTGVFHVATPMDFESKDPENEVIKPTIEGMLGIMKSCAAAKTVRRLVFTSSAGTVNIQEHQLPVYDESCWSDMEFCRAKKMTAWMYFVSKTLAEQAAWKYAKENNIDFITIIPTLVVGPFIMSSMPPSLITALSPITGNEAHYSIIRQGQFVHLDDLCNAHIYLFENPKAEGRYICSSHDCIILDLAKMLREKYPEYNIPTEFKGVDENLKSVCFSSKKLTDLGFEFKYSLEDMFTGAVDTCRAKGLLPPSH 329
               SCOP domains d2c29d_ D: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..hhhhheeeee........hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........ee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee........hhhhhhhhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhh....eeeee..eeeehhhhhhhhhhhh...................ee.hhhhhhh......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c29 D   6 ETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPTNVKKVKHLLDLPKAETHLTLWKADLADEGSFDEAIKGCTGVFHVATPMDFESKDPENEVIKPTIEGMLGIMKSCAAAKTVRRLVFTSSAGTVNIQEHQLPVYDESCWSDMEFCRAKKMTAWMYFVSKTLAEQAAWKYAKENNIDFITIIPTLVVGPFIMSSMPPSLITALSPITGNEAHYSIIRQGQFVHLDDLCNAHIYLFENPKAEGRYICSSHDCIILDLAKMLREKYPEYNIPTEFKGVDENLKSVCFSSKKLTDLGFEFKYSLEDMFTGAVDTCRAKGLLPPSH 329
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    


Chain F from PDB  Type:PROTEIN  Length:326
 aligned with P93799_VITVI | P93799 from UniProtKB/TrEMBL  Length:337

    Alignment length:326
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
         P93799_VITVI     5 SETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPTNVKKVKHLLDLPKAETHLTLWKADLADEGSFDEAIKGCTGVFHVATPMDFESKDPENEVIKPTIEGMLGIMKSCAAAKTVRRLVFTSSAGTVNIQEHQLPVYDESCWSDMEFCRAKKMTAWMYFVSKTLAEQAAWKYAKENNIDFITIIPTLVVGPFIMSSMPPSLITALSPITGNEAHYSIIRQGQFVHLDDLCNAHIYLFENPKAEGRYICSSHDCIILDLAKMLREKYPEYNIPTEFKGVDENLKSVCFSSKKLTDLGFEFKYSLEDMFTGAVDTCRAKGLLPPSHE 330
               SCOP domains d2c29f_ F: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..hhhhheeeee........hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh........ee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee.eee........hhhhhhhhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhh....eeeee..eeeehhhhhhhhhhhh...................ee.hhhhhhhh.....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c29 F   5 SETVCVTGASGFIGSWLVMRLLERGYTVRATVRDPTNVKKVKHLLDLPKAETHLTLWKADLADEGSFDEAIKGCTGVFHVATPMDFESKDPENEVIKPTIEGMLGIMKSCAAAKTVRRLVFTSSAGTVNIQEHQLPVYDESCWSDMEFCRAKKMTAWMYFVSKTLAEQAAWKYAKENNIDFITIIPTLVVGPFIMSSMPPSLITALSPITGNEAHYSIIRQGQFVHLDDLCNAHIYLFENPKAEGRYICSSHDCIILDLAKMLREKYPEYNIPTEFKGVDENLKSVCFSSKKLTDLGFEFKYSLEDMFTGAVDTCRAKGLLPPSHE 330
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C29)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain D,F   (P93799_VITVI | P93799)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0045552    dihydrokaempferol 4-reductase activity    Catalysis of the reaction: cis-3,4-leucopelargonidin + NADP+ = (+)-dihydrokaempferol + NADPH + H+.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  2c29
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  P93799_VITVI | P93799
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  1.1.1.219
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P93799_VITVI | P93799: 2iod 2nnl 3bxx 3c1t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2C29)