PXD061296

PXD061296 is an original dataset announced via ProteomeXchange.

Title	Local and Global Breathing Motions Prime the Access to Buried Binding Site in an Antibiotic-Sequestering Protein
Description	Proteins frequently undergo large-scale conformational excursions in their native ensemble. Such structural transitions are particularly critical for enabling access to binding sites when they are buried in the protein interior. Here, we map the conformational landscape of AlbAS, a natural isoform of the transcription factor AlbA from the gut microbe Klebsiella oxytoca, which sequesters the antibiotic albicidin in a solvent-inaccessible binding tunnel. Combining equilibrium, time-resolved experiments, structural mass spectrometry and calorimetry with statistical modeling, we show that AlbAS displays large differences in local and global stability and dynamics, with ~600-fold difference in unfolding rates across different parts of the structure. Several residues lining the ligand-binding pocket and the inter-sub-domain residues rapidly exchange protons with the solvent in hydrogen-deuterium exchange mass spectrometry experiments, indicative of anisotropic distributions of local stabilities, with the N-terminal subdomain being less stable. The AlbAS conformational landscape is thus quite rugged encompassing numerous partially structured states in equilibrium, including partial unlocking of the N-terminal sub-domain at a time-constant of 6 milliseconds that exposes the binding sites to aid in albicidin binding.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-04_09:30:28.613.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dmitry Loginov
SpeciesList	scientific name: Klebsiella oxytoca; NCBI TaxID: 571;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-27 23:48:55	ID requested
⏵ 1	2025-08-04 09:30:29	announced

10.1021/ACSBIOMEDCHEMAU.5C00081;

submitter keyword: antibiotic sequestration, tryptophan scanning mutagenesis,Protein dynamics, domain duplication, antibiotic resistance

Petr Man
contact affiliation	Institute of Microbiology of the CAS
contact email	pman@biomed.cas.cz
lab head
Dmitry Loginov
contact affiliation	BioCeV - Institute of Microbiology of the CAS
contact email	dloginov@jcu.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061296
     1. Label: PRIDE project
     2. Name: Local and Global Breathing Motions Prime the Access to Buried Binding Site in an Antibiotic-Sequestering Protein