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PDBsum entry 2brt

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protein ligands metals links
Oxidoreductase PDB id
2brt
Jmol
Contents
Protein chain
348 a.a. *
Ligands
AKG
NAR
Metals
FE2
Waters ×128
* Residue conservation analysis
PDB id:
2brt
Name: Oxidoreductase
Title: Anthocyanidin synthase from arabidopsis thaliana complexed with naringenin
Structure: Leucoanthocyanidin dioxygenase. Chain: a. Synonym: ldox, leucocyanidin oxygenase, ans, leucoanthocyan hydroxylase, anthocyanidin synthase. Engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.211     R-free:   0.268
Authors: J.J.Turnbull,I.J.Clifton,R.W.D.Welford,C.J.Schofield
Key ref: R.W.Welford et al. (2005). Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism. Org Biomol Chem, 3, 3117-3126. PubMed id: 16106293
Date:
11-May-05     Release date:   29-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q96323  (LDOX_ARATH) -  Leucoanthocyanidin dioxygenase
Seq:
Struc:
356 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.19  - Leucocyanidin oxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Anthocyanin Biosynthesis
      Reaction: Leucocyanidin + 2-oxoglutarate + O2 = cis- and trans-dihydroquercetins + succinate + CO2 + H2O
Leucocyanidin
Bound ligand (Het Group name = NAR)
matches with 90.91% similarity
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ O(2)
= cis- and trans-dihydroquercetins
+ succinate
+ CO(2)
+ H(2)O
      Cofactor: Iron; L-ascorbate
Iron
L-ascorbate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   7 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
Org Biomol Chem 3:3117-3126 (2005)
PubMed id: 16106293  
 
 
Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism.
R.W.Welford, I.J.Clifton, J.J.Turnbull, S.C.Wilson, C.J.Schofield.
 
  ABSTRACT  
 
During the biosynthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C-ring are catalysed by Fe(ii) and 2-oxoglutarate dependent oxygenases. The reactions catalysed by three of these enzymes; flavone synthase I, flavonol synthase and anthocyanidin synthase (ANS), are formally desaturations. In comparison, flavanone 3beta-hydroxylase catalyses hydroxylation at the C-3 pro-R position of 2S-naringenin. Incubation of ANS with the unnatural substrate (+/-)-naringenin results in predominantly C-3 hydroxylation to give cis-dihydrokaempferol as the major product; trans-dihydrokaempferol and the desaturation product, apigenin are also observed. Labelling studies have demonstrated that some of the formal desaturation reactions catalysed by ANS proceed via initial C-3 hydroxylation followed by dehydration at the active site. We describe analyses of the reaction of ANS with 2S- and 2R-naringenin substrates, including the anaerobic crystal structure of an ANS-Fe-2-oxoglutarate-naringenin complex. Together the results reveal that for the 'natural' C-2 stereochemistry of 2S-naringenin, C-3 hydroxylation predominates (>9 : 1) over desaturation, probably due to the inaccessibility of the C-2 hydrogen to the iron centre. For the 2R-naringenin substrate, desaturation is significantly increased relative to C-3 hydroxylation (ca. 1 : 1); this is probably a result of both the C-3 pro-S and C-2 hydrogen atoms being accessible to the reactive oxidising intermediate in this substrate. In contrast to the hydroxylation-elimination desaturation mechanism for some ANS substrates, the results imply that the ANS catalysed desaturation of 2R-naringenin to form apigenin proceeds with a syn-arrangement of eliminated hydrogen atoms and not via an oxygenated (gem-diol) flavonoid intermediate. Thus, by utilising flavonoid substrates with different C-2 stereochemistries, the balance between C-3 hydroxylation or C-2, C-3 desaturation mechanisms can be altered.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18023053 Y.Yan, Z.Li, and M.A.Koffas (2008).
High-yield anthocyanin biosynthesis in engineered Escherichia coli.
  Biotechnol Bioeng, 100, 126-140.  
17701137 J.Lättig, M.Böhl, P.Fischer, S.Tischer, C.Tietböhl, M.Menschikowski, H.O.Gutzeit, P.Metz, and M.T.Pisabarro (2007).
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design.
  J Comput Aided Mol Des, 21, 473-483.  
17431691 V.Purpero, and G.R.Moran (2007).
The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes.
  J Biol Inorg Chem, 12, 587-601.  
16702218 J.Nakajima, Y.Sato, T.Hoshino, M.Yamazaki, and K.Saito (2006).
Mechanistic study on the oxidation of anthocyanidin synthase by quantum mechanical calculation.
  J Biol Chem, 281, 21387-21398.  
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.