8J5U | pdb_00008j5u

Crystal structure of Mycobacterium tuberculosis OppA complexed with an endogenous oligopeptide

• PDB DOI: https://doi.org/10.2210/pdb8J5U/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv, Mycolicibacterium smegmatis MC2 155
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2023-04-24 Released: 2024-04-03 
• Deposition Author(s): Yang, X., Hu, T., Zhang, B., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.226 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 

Starting Model: in silico

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 31: 1072-1082

• PubMed: 38548954 
• DOI: https://doi.org/10.1038/s41594-024-01256-z
• Primary Citation 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.

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
Laboratory of Structural Biology, Tsinghua University, Beijing, China.
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
Shanghai Clinical Research and Trial Center, Shanghai, China.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane Queensland, Australia.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Shanghai Clinical Research and Trial Center, Shanghai, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, Beijing, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Shanghai Clinical Research and Trial Center, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.52 kDa 
• Atom Count: 4,379 
• Modeled Residue Count: 543 
• Deposited Residue Count: 608 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv1280c	A	599	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv1280c, MTCY50.02
UniProt
Find proteins for P9WGU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGU5  Go to UniProtKB:  P9WGU5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endogenous oligopeptide	B	9	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.226 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.643	α = 90
b = 56.986	β = 122.29
c = 101.902	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Yang, X., Hu, T., Zhang, B., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200996
National Natural Science Foundation of China (NSFC)	China	32171217

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-04-10
  Changes: Database references
• Version 1.2: 2024-07-31
  Changes: Database references