8JA7

Cryo-EM structure of Mycobacterium tuberculosis LpqY-SugABC in complex with trehalose


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose transport system permease protein SugA307Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sugA
Membrane Entity: Yes 
UniProt
Find proteins for P9WG03 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WG03
Entity Groups  
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UniProt GroupP9WG03
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose transport system permease protein SugB274Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sugB
Membrane Entity: Yes 
UniProt
Find proteins for P9WG01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG01 
Go to UniProtKB:  P9WG01
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UniProt GroupP9WG01
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose-binding lipoprotein LpqYC [auth E]468Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: lpqY
Membrane Entity: Yes 
UniProt
Find proteins for P9WGU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGU9 
Go to UniProtKB:  P9WGU9
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UniProt GroupP9WGU9
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose import ATP-binding protein SugCD [auth C],
E [auth D]
393Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: sugC
EC: 7.5.2
Membrane Entity: Yes 
UniProt
Find proteins for P9WQI3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQI3 
Go to UniProtKB:  P9WQI3
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UniProt GroupP9WQI3
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
F
2N/A
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2023-09-27
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references