4OBU

Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine.

Williams, B.B.Van Benschoten, A.H.Cimermancic, P.Donia, M.S.Zimmermann, M.Taketani, M.Ishihara, A.Kashyap, P.C.Fraser, J.S.Fischbach, M.A.

(2014) Cell Host Microbe 16: 495-503

  • DOI: 10.1016/j.chom.2014.09.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several recent studies describe the influence of the gut microbiota on host brain and behavior. However, the mechanisms responsible for microbiota-nervous system interactions are largely unknown. Using a combination of genetics, biochemistry, and cry ...

    Several recent studies describe the influence of the gut microbiota on host brain and behavior. However, the mechanisms responsible for microbiota-nervous system interactions are largely unknown. Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter tryptamine. Although this enzymatic activity is exceedingly rare among bacteria more broadly, analysis of the Human Microbiome Project data demonstrate that at least 10% of the human population harbors at least one bacterium encoding a tryptophan decarboxylase in their gut community. Our results uncover a previously unrecognized enzymatic activity that can give rise to host-modulatory compounds and suggests a potential direct mechanism by which gut microbiota can influence host physiology, including behavior.


    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal-dependent decarboxylase domain protein
E, A, U, G, H, F, B, C
490Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)Mutation(s): 0 
Find proteins for A7B1V0 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9))
Go to UniProtKB:  A7B1V0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, E, F, G, H, U
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 58.630α = 72.85
b = 145.770β = 88.84
c = 165.070γ = 88.30
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release