Structure of Spermidine disinapoyl transferases(SDT) from Arabidopsis thaliana

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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This is version 1.2 of the entry. See complete history


Structural and Biochemical Insights Into Two BAHD Acyltransferases ( At SHT and At SDT) Involved in Phenolamide Biosynthesis.

Wang, C.Li, J.Ma, M.Lin, Z.Hu, W.Lin, W.Zhang, P.

(2020) Front Plant Sci 11: 610118-610118

  • DOI: https://doi.org/10.3389/fpls.2020.610118
  • Primary Citation of Related Structures:  
    6LPV, 6LPW

  • PubMed Abstract: 

    Phenolamides represent one of the largest classes of plant-specialized secondary metabolites and function in diverse physiological processes, including defense responses and development. The biosynthesis of phenolamides requires the BAHD-family acyltransferases, which transfer acyl-groups from different acyl-donors specifically to amines, the acyl-group acceptors. However, the mechanisms of substrate specificity and multisite-acylation of the BAHD-family acyltransferases remain poorly understood. In this study, we provide a structural and biochemical analysis of At SHT and At SDT, two representative BAHD-family members that catalyze the multisite acylation of spermidine but show different product profiles. By determining the structures of At SHT and At SDT and using structure-based mutagenesis, we identified the residues important for substrate recognition in At SHT and At SDT and hypothesized that the acyl acceptor spermidine might adopt a free-rotating conformation in At SHT, which can undergo mono-, di-, or tri-acylation; while the spermidine molecule in At SDT might adopt a linear conformation, which only allows mono- or di-acylation to take place. In addition, through sequence similarity network (SSN) and structural modeling analysis, we successfully predicted and verified the functions of two uncharacterized Arabidopsis BAHD acyltransferases, OAO95042.1 and NP_190301.2, which use putrescine as the main acyl-acceptor. Our work provides not only an excellent starting point for understanding multisite acylation in BAHD-family enzymes, but also a feasible methodology for predicting possible acyl acceptor specificity of uncharacterized BAHD-family acyltransferases.

  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine sinapoyl-CoA acyltransferase
A, B
451Arabidopsis thalianaMutation(s): 0 
Gene Names: SDT
Find proteins for O80467 (Arabidopsis thaliana)
Explore O80467 
Go to UniProtKB:  O80467
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO80467
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPD (Subject of Investigation/LOI)
Query on SPD

Download Ideal Coordinates CCD File 
C7 H19 N3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.989α = 90
b = 103.062β = 90
c = 135.411γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description