PXD067451

PXD067451 is an original dataset announced via ProteomeXchange.

Title	Nanobody-mediated modulation of long RSH enzymes Rel and RelA catalysis by restriction of their conformational landscape
Description	Long RSH enzymes, Rel and RelA, are the master regulators of (p)ppGpp alarmone levels in bacteria. Their catalytic activity is governed by transitions between a compact, hydrolysis-competent (HDON) state and an elongated, synthesis-competent (SYNTHON) state. The equilibrium between these states is modulated by factors such as “starved” ribosomes and regulatory proteins DarB, EIIANTR, ACP and YtfK. Here, we identify and characterize camelid nanobodies that act as selective allosteric modulators by trapping Rel/RelA enzymes in distinct conformational states. Nanobodies that lock the TGS domain of RelA and prevent its activation by deacylated tRNA on starved ribosomes, strongly inhibit (p)ppGpp synthesis and suppress the virulence of E. coli in an animal model. Nb898 stabilizes Rel in the open SYNTHON state, enhancing synthesis activity while suppressing hydrolysis. Conversely, Nb585 traps Rel in a HDON conformation, strongly inhibiting alarmone synthesis while promoting (p)ppGpp hydrolysis. Structural and biochemical analyses reveal that nanobodies, like natural allosteric regulators, act by restricting the RSH enzyme’s conformational landscape. These findings establish nanobodies as powerful tools for dissecting RSH function and provide potential leads for developing protein-based RSH modulators.
HostingRepository	PRIDE
AnnounceDate	2026-04-28
AnnouncementXML	Submission_2026-04-28_12:53:34.138.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chloe Martens
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-18 00:58:53	ID requested
⏵ 1	2026-04-28 12:53:34	announced

Dataset with its publication pending

submitter keyword: structural biology,RSH enzymes, nanobodies

Chloe Martens
contact affiliation	Biochemistry and Structural Biology, Chemistry Department,Université Libre de Bruxelles, Belgium
contact email	chloe.martens@ulb.be
lab head
Chloe Martens
contact affiliation	Universite Libre de Bruxelles
contact email	chloe.martens@ulb.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067451
     1. Label: PRIDE project
     2. Name: Nanobody-mediated modulation of long RSH enzymes Rel and RelA catalysis by restriction of their conformational landscape