8JAA

Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-04


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 

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Literature

Molecular recognition of trehalose and trehalose analogues by Mycobacterium tuberculosis LpqY-SugABC.

Liang, J.Liu, F.Xu, P.Shangguan, W.Hu, T.Wang, S.Yang, X.Xiong, Z.Yang, X.Guddat, L.W.Yu, B.Rao, Z.Zhang, B.

(2023) Proc Natl Acad Sci U S A 120: e2307625120-e2307625120

  • DOI: https://doi.org/10.1073/pnas.2307625120
  • Primary Citation of Related Structures:  
    8JA7, 8JA8, 8JA9, 8JAA, 8JAB, 8JAC, 8JAD

  • PubMed Abstract: 

    Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen Mycobacterium tuberculosis ( Mtb ). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter Mtb . The substrate-binding protein, LpqY, which forms a stable complex with the translocator SugABC, recognizes and captures trehalose and its analogues in the periplasmic space, but the precise molecular mechanism for this process is still not well understood. This study reports a 3.02-Å cryoelectron microscopy structure of trehalose-bound Mtb LpqY-SugABC in the pretranslocation state, a crystal structure of Mtb LpqY in a closed form with trehalose bound and five crystal structures of Mtb LpqY in complex with different trehalose analogues. These structures, accompanied by substrate-stimulated ATPase activity data, reveal how LpqY recognizes and binds trehalose and its analogues, and highlight the flexibility in the substrate binding pocket of LpqY. These data provide critical insights into the design of trehalose analogues that could serve as potential molecular probe tools or as anti-TB drugs.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose-binding lipoprotein LpqY468Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: lpqYRv1235
UniProt
Find proteins for P9WGU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGU9 
Go to UniProtKB:  P9WGU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGU9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.075α = 90
b = 65.808β = 90
c = 143.773γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171217
National Natural Science Foundation of China (NSFC)China32200983

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Data collection, Database references