7DAK

The crystal structure of a serotonin N-acetyltransferase in complex with 5-Methoxytryptamine and acetyl-CoA from Oryza Sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural and Molecular Dynamics Analysis of Plant Serotonin N-Acetyltransferase Reveal an Acid/Base-Assisted Catalysis in Melatonin Biosynthesis.

Liao, L.Zhou, Y.Xu, Y.Zhang, Y.Liu, X.Liu, B.Chen, X.Guo, Y.Zeng, Z.Zhao, Y.

(2021) Angew Chem Int Ed Engl 60: 12020-12026

  • DOI: https://doi.org/10.1002/anie.202100992
  • Primary Citation of Related Structures:  
    6K5M, 7DAI, 7DAJ, 7DAK, 7DAL

  • PubMed Abstract: 

    Serotonin N-acetyltransferase (SNAT) is the key rate-limiting enzyme in melatonin biosynthesis. It mediates melatonin biosynthesis in plants by using serotonin and 5-methoxytryptamine (5-MT), but little is known of its underlying mechanisms. Herein, we present a detailed reaction mechanism of a SNAT from Oryza sativa through combined structural and molecular dynamics (MD) analysis. We report the crystal structures of plant SNAT in the apo and binary/ternary complex forms with acetyl-CoA (AcCoA), serotonin, and 5-MT. OsSNAT exhibits a unique enzymatically active dimeric fold not found in the known structures of arylalkylamine N-acetyltransferase (AANAT) family. The key residues W188, D189, D226, N220, and Y233 located around the active pocket are important in catalysis, confirmed by site-directed mutagenesis. Combined with MD simulations, we hypothesize a novel plausible catalytic mechanism in which D226 and Y233 function as catalytic base and acid during the acetyl-transfer reaction.


  • Organizational Affiliation

    School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serotonin N-acetyltransferase 1, chloroplastic
A, B
166Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: SNAT1GNAT5NSISNATOs05g0481000LOC_Os05g40260OsJ_018182OsJ_18949OSJNBa0095J22.4
EC: 2.3.1.87 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt
Find proteins for Q5KQI6 (Oryza sativa subsp. japonica)
Explore Q5KQI6 
Go to UniProtKB:  Q5KQI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KQI6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.382α = 90
b = 66.815β = 90
c = 83.497γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description