8J5U

Crystal structure of Mycobacterium tuberculosis OppA complexed with an endogenous oligopeptide

Summary for 8J5U

• Entry DOI: 10.2210/pdb8j5u/pdb
• Descriptor: Uncharacterized protein Rv1280c, Endogenous oligopeptide (3 entities in total)
• Functional Keywords: oppa, oligopeptide binding protein, cluster c sbp, mycobacterium tuberculosis, peptide binding protein
• Biological source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv); More
• Total number of polymer chains: 2
• Total formula weight: 65523.31

Authors

Yang, X.,Hu, T.,Zhang, B.,Rao, Z. (deposition date: 2023-04-24, release date: 2024-04-03, Last modification date: 2024-07-31)

Primary citation

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.
An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Nat.Struct.Mol.Biol., 31:1072-1082, 2024

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.

PubMed: 38548954
DOI: 10.1038/s41594-024-01256-z

Experimental method

X-RAY DIFFRACTION (1.98 Å)