4A6D

Crystal structure of human N-acetylserotonin methyltransferase (ASMT) in complex with SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure and Functional Mapping of Human Asmt, the Last Enzyme of the Melatonin Synthesis Pathway.

Botros, H.G.Legrand, P.Pagan, C.Bondet, V.Weber, P.Ben-Abdallah, M.Lemiere, N.Huguet, G.Bellalou, J.Maronde, E.Beguin, P.Haouz, A.Shepard, W.Bourgeron, T.

(2013) J.Pineal Res. 54: 46

  • DOI: 10.1111/j.1600-079X.2012.01020.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Melatonin is a synchronizer of many physiological processes. Abnormal melatonin signaling is associated with human disorders related to sleep, metabolism, and neurodevelopment. Here, we present the X-ray crystal structure of human N-acetyl serotonin ...

    Melatonin is a synchronizer of many physiological processes. Abnormal melatonin signaling is associated with human disorders related to sleep, metabolism, and neurodevelopment. Here, we present the X-ray crystal structure of human N-acetyl serotonin methyltransferase (ASMT), the last enzyme of the melatonin biosynthesis pathway. The polypeptide chain of ASMT consists of a C-terminal domain, which is typical of other SAM-dependent O-methyltransferases, and an N-terminal domain, which intertwines several helices with another monomer to form the physiologically active dimer. Using radioenzymology, we analyzed 20 nonsynonymous variants identified through the 1000 genomes project and in patients with neuropsychiatric disorders. We found that the majority of these mutations reduced or abolished ASMT activity including one relatively frequent polymorphism in the Han Chinese population (N17K, rs17149149). Overall, we estimate that the allelic frequency of ASMT deleterious mutations ranges from 0.66% in Europe to 2.97% in Asia. Mapping of the variants on to the 3-dimensional structure clarifies why some are harmful and provides a structural basis for understanding melatonin deficiency in humans.


    Organizational Affiliation

    Institut Pasteur, Human Genetics and Cognitive Functions Unit, Paris, France CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur, Paris, France University Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, Gif-sur-Yvette, France Institut Pasteur, Plate forme 5, 25 rue Dr. Roux, Paris, France Institut Pasteur, Plate forme 6, CNRS-UMR3528, 25 rue Dr. Roux, Paris, France Institute for Anatomy III, Goethe University, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROXYINDOLE O-METHYLTRANSFERASE
A
353Homo sapiensMutation(s): 0 
Gene Names: ASMT
EC: 2.1.1.4
Find proteins for P46597 (Homo sapiens)
Go to Gene View: ASMT
Go to UniProtKB:  P46597
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 170.400α = 90.00
b = 170.400β = 90.00
c = 123.320γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references