6LH1

Crystal structure of a cysteine-pair mutant (Y113C-P190C) of a bacterial bile acid transporter trapped in an outward-facing conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


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Literature

An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter.

Wang, X.Lyu, Y.Ji, Y.Sun, Z.Zhou, X.

(2021) Acta Crystallogr D Struct Biol 77: 108-116

  • DOI: 10.1107/S205979832001517X
  • Primary Citation of Related Structures:  
    7CYG, 7CYK, 6LH1

  • PubMed Abstract: 
  • Apical sodium-dependent bile acid transporter (ASBT) mediates the uptake of bile acids from the ileum lumen into enterocytes and presents a potential target for the treatment of several metabolic diseases, including type 2 diabetes. It has been proposed that the underlying mechanism for transport by ASBT is an elevator-style alternating-access model, which was deduced mainly by comparing high-resolution structures of two bacterial ASBT homologs (ASBT NM from Neisseria meningitides and ASBT Yf from Yersinia frederiksenii) in different conformations ...

    Apical sodium-dependent bile acid transporter (ASBT) mediates the uptake of bile acids from the ileum lumen into enterocytes and presents a potential target for the treatment of several metabolic diseases, including type 2 diabetes. It has been proposed that the underlying mechanism for transport by ASBT is an elevator-style alternating-access model, which was deduced mainly by comparing high-resolution structures of two bacterial ASBT homologs (ASBT NM from Neisseria meningitides and ASBT Yf from Yersinia frederiksenii) in different conformations. However, one important issue is that the only outward-facing structure (PDB entry 4n7x) was obtained with an Na + -binding site mutant of ASBT Yf , which severely cripples its transport function, and therefore the physiological relevance of the conformation in PDB entry 4n7x requires further careful evaluation. Here, another crystal structure is reported of ASBT Yf that was captured in a state closely resembling the conformation in PDB entry 4n7x using an engineered disulfide bridge. The introduced cysteine mutations avoided any proposed Na + - or substrate-binding residues, and the resulting mutant retained both structural and functional integrity and behaved similarly to wild-type ASBT Yf . These data support the hypothesis that the PDB entry 4n7x-like structure represents a functional outward-facing conformation of ASBT Yf in its transport cycle.


    Organizational Affiliation

    Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transporter, sodium/bile acid symporter family A312Yersinia frederikseniiMutation(s): 2 
Gene Names: NCTC11470_02445
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Apical Sodium-Dependent Bile Acid Transporters (ASBT)
Protein: 
Bacterial homologue of ASBT (ASBTYf), cysteine-pair mutant (Y113C-P190C), outward facing state
Find proteins for A0A380PV03 (Yersinia frederiksenii)
Explore A0A380PV03 
Go to UniProtKB:  A0A380PV03
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A6L
Query on A6L

Download Ideal Coordinates CCD File 
A
2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-KTKRTIGZSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.366α = 90
b = 77.005β = 90
c = 193.114γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770783

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references