PXD063722

PXD063722 is an original dataset announced via ProteomeXchange.

Title	Structural mechanisms of allosteric regulation in the human cis-prenyltransferase complex
Description	Human cis-prenyltransferase (hcis-PT) synthesizes long-chain isoprenoids essential for N-linked protein glycosylation. This heteromeric complex comprises the catalytic subunit DHDDS and the regulatory Nogo-B receptor (NgBR). Although NgBR dramatically enhances DHDDS activity, the molecular basis for this allosteric regulation remains unclear. Here, we combined crystallography, hydrogen-deuterium exchange mass spectrometry (HDX-MS), molecular dynamics simulations, and network analysis to uncover the structural dynamics and communication pathways within hcis-PT. By solving the apo structure of hcis-PT, we reveal only a localized flexibility at the active site and the NgBR C-terminus. However, HDX-MS demonstrated widespread substrate-induced stabilization, particularly at the NgBR βD–βE loop, highlighting it as an allosteric hub. Functional mutagenesis scanning identified NgBRS249 as critical for enzymatic activity, independent of structural perturbations. Network analysis of MD simulations pinpointed this residue as a central node in inter-subunit communication, with perturbations disrupting downstream allosteric pathways, altering enzymatic activity. Our findings reveal a dynamic regulatory network centered at the inter-subunit interface, wherein specific NgBR residues modulate DHDDS activity through allosteric signaling. This work elucidates a conserved mechanism of subunit coordination in long-chain cis-prenyltransferases and suggests novel avenues for therapeutic targeting of hcis-PT-related disorders.
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-20_05:52:40.150.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petr Man
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-07 05:40:55	ID requested
⏵ 1	2025-10-20 05:52:40	announced

Dataset with its publication pending

ProteomeXchange project tag: Hydrogen Deuterium Exchange (HDX-MS)

submitter keyword: Nogo-B receptor, allosteric regulation, Dehydrodolichyl diphosphate synthase,cis-prenyltransferase, DHDDS, N-linked glycosylation, molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, network analysis, NgBR

Petr Man
contact affiliation	Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic
contact email	pman@biomed.cas.cz
lab head
Petr Man
contact affiliation	Institute of Microbiology of the CAS
contact email	pman@biomed.cas.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063722
     1. Label: PRIDE project
     2. Name: Structural mechanisms of allosteric regulation in the human cis-prenyltransferase complex