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Structure paper

TitleAn oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateMar 28, 2024
AuthorsXiaolin Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Zhenli Lin / Yao Zhao / Xiaoting Zhou / Yan Gao / Shan Sun / Xiuna Yang / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang /
PubMed AbstractOligopeptide 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 ...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.
External linksNat Struct Mol Biol / PubMed:38548954
MethodsEM (single particle) / X-ray diffraction
Resolution1.98 - 3.28 Å
Structure data

35990

8j5q

EMDB-35990, PDB-8j5q:
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-translocation state
Method: EM (single particle) / Resolution: 3.25 Å

35991

8j5r

EMDB-35991, PDB-8j5r:
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state
Method: EM (single particle) / Resolution: 3.28 Å

35992

8j5s

EMDB-35992, PDB-8j5s:
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
Method: EM (single particle) / Resolution: 3.0 Å

35993

8j5t

EMDB-35993, PDB-8j5t:
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
Method: EM (single particle) / Resolution: 2.98 Å

PDB-8j5u:
Crystal structure of Mycobacterium tuberculosis OppA complexed with an endogenous oligopeptide
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-HOH:
WATER / Water

Source
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
  • mycolicibacterium smegmatis mc2 155 (bacteria)
KeywordsMEMBRANE PROTEIN / OppABCD / Type I ABC importer / Oligopeptide permease / Mycobacterium tuberculosis / AMPPNP-Mg / Pre-catalytic intermediate state / ATP-Mg / Occluded state / PEPTIDE BINDING PROTEIN / OppA / Oligopeptide binding protein / Cluster C SBP

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