8VRX | pdb_00008vrx

Bile salt hydrolase from Arthrobacter citreus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.172 (Depositor), 0.171 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8VRX

This is version 1.1 of the entry. See complete history

Literature

Structural and functional analysis of a bile salt hydrolase from the bison microbiome.

Asar, R.Dhindwal, P.Ruzzini, A.

(2024) J Biological Chem 300: 107769-107769

  • DOI: https://doi.org/10.1016/j.jbc.2024.107769
  • Primary Citation Related Structures: 
    8VRX, 8VSY

  • PubMed Abstract: 

    The bile salt hydrolases (BSHs) are significant constituents of animal microbiomes. An evolving appreciation of their roles in health and disease has established them as targets of pharmacological inhibition. These bacterial enzymes belong to the N-terminal nucleophile superfamily and are best known to catalyze the deconjugation of glycine or taurine from bile salts to release bile acid substrates for transformation and or metabolism in the gastrointestinal tract. Here, we identify and describe the BSH from a common member of the Plains bison microbiome, Arthrobacter citreus (BSH Ac ). Steady-state kinetic analyses demonstrated that BSH Ac is a broad-spectrum hydrolase with a preference for glycine-conjugates and deoxycholic acid (DCA). Second-order rate constants (k cat /K M ) for BSH Ac -catalyzed reactions of relevant bile salts-glyco- and tauro-conjugates of cholic acid and DCA- varied by ∼30-fold and measured between 1.4 × 10 5 and 4.3 × 10 6  M -1 s -1 . Interestingly, a pan-BSH inhibitor named AAA-10 acted as a slow irreversible inhibitor of BSH Ac with a rate of inactivation (k inact ) of ∼2 h -1 and a second order rate constant (k inact /K I ) of ∼24 M -1 s -1 for the process. Structural characterization of BSH Ac reacted with AAA-10 showed covalent modification of the N-terminal cysteine nucleophile, providing molecular details for an enzyme-stabilized product formed from this mechanism-based inhibitor's α-fluoromethyl ketone warhead. Structural comparison of the BSHs and BSH:inhibitor complexes highlighted the plasticity of the steroid-binding site, including a flexible loop that is variable across well-studied BSHs.


  • Organizational Affiliation
    • Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.

Macromolecule Content 

  • Total Structure Weight: 72.26 kDa 
  • Atom Count: 5,735 
  • Modeled Residue Count: 633 
  • Deposited Residue Count: 644 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile Salt Hydrolase
A, B
322Arthrobacter citreusMutation(s): 0 
EC: 3.5.1.24
UniProt
Find proteins for A0AAN0NPC4 (Arthrobacter citreus)
Explore A0AAN0NPC4 
Go to UniProtKB:  A0AAN0NPC4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN0NPC4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
T [auth B],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
R [auth B],
S [auth B],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
F [auth A]
H [auth A]
L [auth A]
N [auth A]
D [auth A],
F [auth A],
H [auth A],
L [auth A],
N [auth A],
O [auth A],
P [auth A],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A],
M [auth A],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.787α = 90
b = 44.071β = 111.07
c = 86.592γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references, Structure summary