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(-) Description

Title :  STRUCTURE OF THE BINARY COMPLEX LEUCOANTHOCYANIDIN REDUCTASE - NADPH FROM VITIS VINIFERA
 
Authors :  C. Mauge, M. Gargouri, B. L. D'Estaintot, T. Granier, B. Gallois
Date :  07 Jul 09  (Deposition) - 23 Feb 10  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Short Chain Dehydrogenase Reductase, Flavonoid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Mauge, T. Granier, B. L. D'Estaintot, M. Gargouri, C. Manigand, J. M. Schmitter, J. Chaudiere, B. Gallois
Crystal Structure And Catalytic Mechanism Of Leucoanthocyanidin Reductase From Vitis Vinifera.
J. Mol. Biol. V. 397 1079 2010
PubMed-ID: 20138891  |  Reference-DOI: 10.1016/J.JMB.2010.02.002

(-) Compounds

Molecule 1 - PUTATIVE LEUCOANTHOCYANIDIN REDUCTASE 1
    Chains: A
    EC Number: 1.17.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETGB1A
    Expression System Strain: BL21[DE3]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LAR1
    Organism Common: WINE GRAPE
    Organism Scientific: VITIS VINIFERA
    Organism Taxid: 29760

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , THR A:19 , GLY A:20 , PHE A:21 , ILE A:22 , ARG A:42 , LEU A:68 , ILE A:69 , ASN A:70 , THR A:90 , VAL A:91 , GLY A:92 , SER A:95 , ASP A:98 , SER A:118 , GLU A:119 , PHE A:120 , LYS A:140 , ASN A:160 , ILE A:162 , ACY A:360 , HOH A:361 , HOH A:416 , HOH A:445 , HOH A:459 , HOH A:581 , HOH A:640BINDING SITE FOR RESIDUE NDP A 350
2AC2SOFTWAREGLY A:121 , HIS A:122 , TYR A:137 , PHE A:272 , NDP A:350 , HOH A:364BINDING SITE FOR RESIDUE ACY A 360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I6I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:131 -Pro A:132
2Ile A:264 -Pro A:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I6I)

(-) Exons   (0, 0)

(no "Exon" information available for 3I6I)

(-) Sequences/Alignments

Asymmetric/Biological 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 A from PDB  Type:PROTEIN  Length:302
 aligned with Q4W2K4_VITVI | Q4W2K4 from UniProtKB/TrEMBL  Length:346

    Alignment length:307
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
         Q4W2K4_VITVI    11 GRVLIAGATGFIGQFVATASLDAHRPTYILARPGPRSPSKAKIFKALEDKGAIIVYGLINEQEAMEKILKEHEIDIVVSTVGGESILDQIALVKAMKAVGTIKRFLPSEFGHDVNRADPVEPGLNMYREKRRVRQLVEESGIPFTYICCNSIASWPYYNNIHPSEVLPPTDFFQIYGDGNVKAYFVAGTDIGKFTMKTVDDVRTLNKSVHFRPSCNCLNINELASVWEKKIGRTLPRVTVTEDDLLAAAGENIIPQSVVAAFTHDIFIKGCQVNFSIDGPEDVEVTTLYPEDSFRTVEECFGEYIVK 317
               SCOP domains d3i6ia_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3i6iA01 A:11-158,A:198-220,A:286-299 NAD(P)-binding Rossmann-like Domain                                                                            3i6iA02 A:15     9-197,A:221-285,A:300-3i6iA01                3i6iA02 A:159-197,A:221-285,A:300-317                            3i6iA01       3i6iA02            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh...eee...............hhhhhhhhhhhhhhhhhhh....eeee..ee........-----.......eeee......eeeehhhhhhhhhhhhhhhhhhh.eeee..hhh.eehhhhhhhhhhhhhh....eeeehhhhhhhhhhh...hhhhhhhhhhhhhh.............eeehhhhh......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6i A  11 GRVLIAGATGFIGQFVATASLDAHRPTYILARPGPRSPSKAKIFKALEDKGAIIVYGLINEQEAMEKILKEHEIDIVVSTVGGESILDQIALVKAMKAVGTIKRFLPSEFGHDVNRADPVEPGLNMYREKRRVRQLVEESGIPFTYICCNSIASWPYYNN-----VLPPTDFFQIYGDGNVKAYFVAGTDIGKFTMKTVDDVRTLNKSVHFRPSCNCLNINELASVWEKKIGRTLPRVTVTEDDLLAAAGENIIPQSVVAAFTHDIFIKGCQVNFSIDGPEDVEVTTLYPEDSFRTVEECFGEYIVK 317
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     | 180       190       200       210       220       230       240       250       260       270       280       290       300       310       
                                                                                                                                                                                         170   176
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I6I)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4W2K4_VITVI | Q4W2K4)
molecular function
    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.

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  1.17.1.3
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 Related Entries

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

UniProtKB/TrEMBL
        Q4W2K4_VITVI | Q4W2K4: 3i52 3i5m 3i6q

(-) Related Entries Specified in the PDB File

3i52 TERNARY COMPLEX STRUCTURE OF LEUCOANTHOCYANIDIN REDUCTASE
3i5m STRUCTURE OF APO FORM OF LEUCOANTHOCYANIDIN REDUCTASE