Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 7, Page 1072-1082, Year 2024
Publish date	Mar 28, 2024
Authors	Xiaolin 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 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 ...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 links	Nat Struct Mol Biol / PubMed:38548954
Methods	EM (single particle) / X-ray diffraction
Resolution	1.98 - 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 ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-HOH: WATER
Source	mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria) mycolicibacterium smegmatis mc2 155 (bacteria)
Keywords	MEMBRANE 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