7DEX

Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase H174A mutant with caffeoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Literature

Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin.

Murayama, K.Kato-Murayama, M.Sato, T.Hosaka, T.Ishiguro, K.Mizuno, T.Kitao, K.Honma, T.Yokoyama, S.Tanaka, Y.Shirouzu, M.

(2021) Phytochemistry 186: 112727-112727

  • DOI: https://doi.org/10.1016/j.phytochem.2021.112727
  • Primary Citation of Related Structures:  
    7DEV, 7DEX

  • PubMed Abstract: 

    The acylation of anthocyanins contributes to their structural diversity. Aromatic acylation is responsible for the blue color of anthocyanins and certain flowers. Aromatic acyltransferase from Gentiana triflora Pall. (Gentianaceae) (Gt5,3'AT) catalyzes the acylation of glucosyl moieties at the 5 and 3' positions of anthocyanins. Anthocyanin acyltransferase transfers an acyl group to a single position, such that Gt5,3'AT possesses a unique enzymatic activity. Structural investigation of this aromatic acyl group transfer is fundamental to understand the molecular mechanism of the acylation of double positions. In this study, structural analyses of Gt5,3'AT were conducted to identify the underlying mechanism. The crystal structure indicated that Gt5,3'AT shares structural similarities with other BAHD family enzymes, consisting of N and C terminal lobes. Structural comparison revealed that acyl group preference (aromatic or aliphatic) for the enzymes was determined by four amino acid positions, which are well conserved in aromatic and aliphatic CoA-binding acyltransferases. Although a complex structure with anthocyanins was not obtained, the binding of delphinidin 3,5,3'-triglucoside to Gt5,3'AT was investigated by evaluating the molecular dynamics. The simulation indicated that acyl transfer by Gt5,3'AT preferentially occurs at the 5-position rather than at the 3'-position, with interacting amino acids that are mainly located in the C-terminal lobe. Subsequent assays of chimeric enzymes (exchange of the N-terminal lobe and the C-terminal lobe between Gt5,3'AT and lisianthus anthocyanin 5AT) demonstrated that acyl transfer selectivity may be caused by the C-terminal lobe.


  • Organizational Affiliation

    Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, 980-8575, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anthocyanin 5-aromatic acyltransferase465Gentiana trifloraMutation(s): 1 
EC: 2.3.1.153
UniProt
Find proteins for Q9ZWR8 (Gentiana triflora)
Explore Q9ZWR8 
Go to UniProtKB:  Q9ZWR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZWR8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H5L (Subject of Investigation/LOI)
Query on H5L

Download Ideal Coordinates CCD File 
B [auth A]S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (E)-3-[3,4-bis(oxidanyl)phenyl]prop-2-enethioate
C30 H42 N7 O19 P3 S
QHRGJMIMHCLHRG-ZSELIEHESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.858α = 90
b = 117.894β = 90
c = 184.058γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description