PXD059315

PXD059315 is an original dataset announced via ProteomeXchange.

Title	Molecular basis of vitamin K driven γ-carboxylation at membrane interface
Description	The γ-carboxylation of glutamate residues enables Ca2+-mediated membrane assembly of protein complexes that support broad physiological functions including hemostasis, calcium homeostasis, immune response, and endocrine regulation. Modulating γ-carboxylation level provides prevalent treatments for hemorrhagic and thromboembolic diseases. This unique posttranslational modification requires vitamin K hydroquinone (KH2) to drive highly demanding reactions catalyzed by the membrane-integrated γ-carboxylase (VKGC). To decipher underlying mechanisms, we determined cryo-electron microscopy structures of human VKGC in unbound form, with KH2 and four hemostatic and non-hemostatic proteins possessing propeptides and glutamate-rich domains in different carboxylation states. VKGC recognizes substrate proteins via knob-and-hole interactions with propeptides, thereby bringing tethered glutamate-containing segments for processive carboxylation within a large chamber that provides steric control. Propeptide binding also triggers a global conformational change to signal VKGC activation. Through sequential deprotonation and KH2 epoxidation, VKGC generates free hydroxide ion as an exceptionally strong base required to deprotonate the γ-carbon of glutamate for CO2 addition. The diffusion of this superbase, protected and guided by a sealed hydrophobic tunnel, elegantly resolves the challenge of coupling KH2 epoxidation to γ-carboxylation across the membrane interface. These structural insights and extensive functional experiments advance membrane enzymology and propel the development of novel treatments for γ-carboxylation disorders.
HostingRepository	PRIDE
AnnounceDate	2026-01-26
AnnouncementXML	Submission_2026-01-25_16:08:36.755.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aaron Ammerman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	carboxylated residue; L-gamma-carboxyglutamic acid; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-30 14:00:38	ID requested
⏵ 1	2026-01-25 16:08:37	announced

10.1038/s41422-025-01161-0;

Cao Q, Fan J, Ammerman A, Awasthi S, Lin Z, Mierxiati S, Chen H, Xu J, Garcia BA, Liu B, Li W, -carboxylation of osteocalcin. Cell Res, 35(10):735-749(2025) [pubmed]

submitter keyword: Human, Electron Microscopy, Cryo-EM, Post-Translational Modifications, LC-MS/MS

Dr Weikai Li
contact affiliation	Department of Biochemistry Biophysics and Structural Biology, Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri, United States
contact email	weikai@wustl.edu
lab head
Aaron Ammerman
contact affiliation	Washington University in St. Louis - Li Lab
contact email	a.ammerman@wustl.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD059315

PRIDE project URI

• PRIDE
  1. PXD059315
     1. Label: PRIDE project
     2. Name: Molecular basis of vitamin K driven γ-carboxylation at membrane interface