8J5U

Crystal structure of Mycobacterium tuberculosis OppA complexed with an endogenous oligopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.

Yang, X.Hu, T.Liang, J.Xiong, Z.Lin, Z.Zhao, Y.Zhou, X.Gao, Y.Sun, S.Yang, X.Guddat, L.W.Yang, H.Rao, Z.Zhang, B.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01256-z
  • Primary Citation of Related Structures:  
    8J5Q, 8J5R, 8J5S, 8J5T, 8J5U

  • PubMed Abstract: 

    Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. yangxl@shanghaitech.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Rv1280c599Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1280cMTCY50.02
UniProt
Find proteins for P9WGU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGU5 
Go to UniProtKB:  P9WGU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGU5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endogenous oligopeptide9Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.643α = 90
b = 56.986β = 122.29
c = 101.902γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200996
National Natural Science Foundation of China (NSFC)China32171217

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references