8BLT

Structure of Lactobacillus salivarius (Ls) bile salt hydrolase(BSH) in complex with taurocholate (TCA)

PDB DOI: https://doi.org/10.2210/pdb8BLT/pdb

Classification: HYDROLASE
Organism(s): Ligilactobacillus salivarius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-10 Released: 2023-03-08
Deposition Author(s): Karlov, D.S., Long, S.L., Zeng, X., Xu, F., Lal, K., Cao, L., Hayoun, K., Lin, J., Joyce, S.A., Tikhonova, I.G.
Funding Organization(s): National Institute of Food and Agriculture (NIFA, United States), Other government, Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213
R-Value Work: 0.180
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Characterization of the mechanism of bile salt hydrolase substrate specificity by experimental and computational analyses.

Karlov, D.S., Long, S.L., Zeng, X., Xu, F., Lal, K., Cao, L., Hayoun, K., Lin, J., Joyce, S.A., Tikhonova, I.G.

(2023) Structure 31: 629

PubMed: 36963397 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2023.02.014
Primary Citation of Related Structures:
8BLS, 8BLT

PubMed Abstract:
Bile salt hydrolases (BSHs) are currently being investigated as target enzymes for metabolic regulators in humans and as growth promoters in farm animals. Understanding structural features underlying substrate specificity is necessary for inhibitor design. Here, we used a multidisciplinary workflow including mass spectrometry, mutagenesis, molecular dynamic simulations, machine learning, and crystallography to demonstrate substrate specificity in Lactobacillus salivarius BSH, the most abundant enzyme in human and farm animal intestines. We show the preference of substrates with a taurine head and a dehydroxylated sterol ring for hydrolysis. A regression model that correlates the relative rates of hydrolysis of various substrates in various enzyme mutants with the residue-substrate interaction energies guided the identification of structural determinants of substrate binding and specificity. In addition, we found T208 from another BSH protomer regulating the hydrolysis. The designed workflow can be used for fast and comprehensive characterization of enzymes with a broad range of substrates.

Organizational Affiliation

School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK.

Macromolecule Content

Total Structure Weight: 298.61 kDa
Atom Count: 21,507
Modelled Residue Count: 2,555
Deposited Residue Count: 2,600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile salt hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	325	Ligilactobacillus salivarius	Mutation(s): 0
UniProt
Find proteins for J7H3P9 (Ligilactobacillus salivarius) Explore J7H3P9 Go to UniProtKB: J7H3P9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J7H3P9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TCH (Subject of Investigation/LOI) Query on TCH Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain P [auth H] MOL2 format, chain J [auth B] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	TAUROCHOLIC ACID C₂₆ H₄₅ N O₇ S WBWWGRHZICKQGZ-HZAMXZRMSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.759	α = 90
b = 94.605	β = 90.26
c = 168.215	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institute of Food and Agriculture (NIFA, United States)	United States	2018-67015-27475
Other government		05935-NAGpro
Other government		DAFM 17-RD-US-ROI
Other government		KJCX20220422
Engineering and Physical Sciences Research Council	United Kingdom	EP/R029407/1 and EP/W03204X/1