8SL7 | pdb_00008sl7

Butyricicoccus sp. BIOML-A1 tryptophanase complex with (3S) ALG-05

• PDB DOI: https://doi.org/10.2210/pdb8SL7/pdb

• Classification: LYASE
• Organism(s): Butyricicoccus sp. BIOML-A1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-21 Released: 2023-08-23 
• Deposition Author(s): Graboski, A.L., Redinbo, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate.

Graboski, A.L., Kowalewski, M.E., Simpson, J.B., Cao, X., Ha, M., Zhang, J., Walton, W.G., Flaherty, D.P., Redinbo, M.R.

(2023) Cell Chem Biol 30: 1402-1413.e7

• PubMed: 37633277 
• DOI: https://doi.org/10.1016/j.chembiol.2023.07.015
• Primary Citation Related Structures: 
  8SBG, 8SIJ, 8SL7


• PubMed Abstract: 
  

  Indoxyl sulfate is a microbially derived uremic toxin that accumulates in late-stage chronic kidney disease and contributes to both renal and cardiovascular toxicity. Indoxyl sulfate is generated by the metabolism of indole, a compound created solely by gut microbial tryptophanases. Here, we characterize the landscape of tryptophanase enzymes in the human gut microbiome and find remarkable structural and functional similarities across diverse taxa. We leverage this homology through a medicinal chemistry campaign to create a potent pan-inhibitor, (3S) ALG-05, and validate its action as a transition-state analog. (3S) ALG-05 successfully reduces indole production in microbial culture and displays minimal toxicity against microbial and mammalian cells. Mice treated with (3S) ALG-05 show reduced cecal indole and serum indoxyl sulfate levels with minimal changes in other tryptophan-metabolizing pathways. These studies present a non-bactericidal pan-inhibitor of gut microbial tryptophanases with potential promise for reducing indoxyl sulfate in chronic kidney disease.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 260.64 kDa 
• Atom Count: 17,306 
• Modeled Residue Count: 2,171 
• Deposited Residue Count: 2,276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanase	A, B, C, D	569	Butyricicoccus sp. BIOML-A1	Mutation(s): 0  Gene Names: GT642_04165

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BY3 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(E)-3-[(3S)-3-chloro-2-oxo-2,3-dihydro-1H-indol-3-yl]-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine C19 H19 Cl N3 O8 P BXXCZCGSFDLCHB-ABVQHWRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.64	α = 65.24
b = 93.951	β = 88.01
c = 105.604	γ = 74.3

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Graboski, A.L., Redinbo, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135218
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137286

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Database references