Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo)

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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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: https://doi.org/10.1016/j.chom.2014.09.001
  • Primary Citation of Related Structures:  
    4OBU, 4OBV

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal-dependent decarboxylase domain protein490Mediterraneibacter gnavus ATCC 29149Mutation(s): 0 
Gene Names: RUMGNA_01526
Find proteins for A7B1V0 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9))
Explore A7B1V0 
Go to UniProtKB:  A7B1V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7B1V0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.63α = 72.85
b = 145.77β = 88.84
c = 165.07γ = 88.3
Software Package:
Software NamePurpose
Blu-Icedata collection
xia2data scaling
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations