7DAL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.551α = 90
b = 66.803β = 90
c = 81.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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