4OBV

Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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. Electronic address: fischbach@fischbachgroup.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxal-dependent decarboxylase domain proteinD [auth A],
C [auth B],
B [auth C],
A [auth D]
490[Ruminococcus] gnavus ATCC 29149Mutation(s): 0 
Gene Names: RUMGNA_01526
EC: 4.1.1.105
UniProt
Find proteins for A7B1V0 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9))
Explore A7B1V0 
Go to UniProtKB:  A7B1V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7B1V0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3SO
Query on 3SO

Download Ideal Coordinates CCD File 
F [auth D],
I [auth B],
J [auth A],
L [auth A]
{5-hydroxy-4-[(1E)-4-(1H-indol-3-yl)-3-oxobut-1-en-1-yl]-6-methylpyridin-3-yl}methyl dihydrogen phosphate
C19 H19 N2 O6 P
UHCJSBYGRGJECF-VOTSOKGWSA-N
 Ligand Interaction
2SU
Query on 2SU

Download Ideal Coordinates CCD File 
E [auth D],
G [auth C],
H [auth B],
K [auth A]
alpha-(fluoromethyl)-D-tryptophan
C12 H13 F N2 O2
BZEQVHKJCVLJMC-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.03α = 90
b = 135.03β = 90
c = 249.8γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
xia2data scaling
PHENIXrefinement
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