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TitleStructure and mechanism of vitamin-K-dependent γ-glutamyl carboxylase.
Journal, issue, pagesNature, Vol. 639, Issue 8055, Page 808-815, Year 2025
Publish dateJan 29, 2025
AuthorsRong Wang / Baozhi Chen / Nadia Elghobashi-Meinhardt / Jian-Ke Tie / Alyssa Ayala / Ning Zhou / Xiaofeng Qi /
PubMed Abstractγ-Glutamyl carboxylase (GGCX) is the sole identified enzyme that uses vitamin K (VK) as a cofactor in humans. This protein catalyses the oxidation of VK hydroquinone to convert specific glutamate ...γ-Glutamyl carboxylase (GGCX) is the sole identified enzyme that uses vitamin K (VK) as a cofactor in humans. This protein catalyses the oxidation of VK hydroquinone to convert specific glutamate residues to γ-carboxyglutamate residues in VK-dependent proteins (VDPs), which are involved in various essential biological processes and diseases. However, the working mechanism of GGCX remains unclear. Here we report three cryogenic electron microscopy structures of human GGCX: in the apo state, bound to osteocalcin (a VDP) and bound to VK. The propeptide of the VDP binds to the lumenal domain of GGCX, which stabilizes transmembrane helices 6 and 7 of GGCX to create the VK-binding pocket. After binding of VK, residue Lys218 in GGCX mediates the oxidation of VK hydroxyquinone, which leads to the deprotonation of glutamate residues and the construction of γ-carboxyglutamate residues. Our structural observations and results from binding and cell biological assays and molecular dynamics simulations show that a cholesterol molecule interacts with the transmembrane helices of GGCX to regulate its protein levels in cells. Together, these results establish a link between cholesterol metabolism and VK-dependent pathways.
External linksNature / PubMed:39880952
MethodsEM (single particle)
Resolution2.95 - 3.63 Å
Structure data

44912

9bum

EMDB-44912, PDB-9bum:
Structure of gamma-glutamyl carboxylase (GGCX)
Method: EM (single particle) / Resolution: 3.63 Å

44917

9bur

EMDB-44917, PDB-9bur:
Structure of GGCX-BGP complex
Method: EM (single particle) / Resolution: 2.95 Å

44924

9bux

EMDB-44924, PDB-9bux:
Structure of GGCX-BGP-menaquinone-4 epoxide complex
Method: EM (single particle) / Resolution: 3.06 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

PDB-1at1:
CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / LYASE / vitamin K cycle / LYASE/SUBSTRATE / LYASE-SUBSTRATE complex

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