Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural insight into bicarbonate-mediated carboxylation by human vitamin K-dependent carboxylase.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 10480, Year 2025
Publish date	Nov 25, 2025
Authors	Ke Wu / Zheng Wang / Deqiang Yao / Shaobai Li / Xiaozhu Wang / Yuanyuan Zhang / Mi Cao / Yafeng Shen / Shunpeng Xing / Jian Wu / Ming Lei / Pengfei Lan /
PubMed Abstract	Vitamin K-dependent (VKD) carboxylation, mediated by γ-glutamyl carboxylase (GGCX), is essential for the maturation of VKD proteins involved in critical physiological processes such as blood ...Vitamin K-dependent (VKD) carboxylation, mediated by γ-glutamyl carboxylase (GGCX), is essential for the maturation of VKD proteins involved in critical physiological processes such as blood clotting, vascular calcification and bone metabolism. Here, we present cryo-electron microscopic structures of human GGCX alone and in complex with VKD proteins, vitamin K, and inhibitor anisindione. GGCX specifically recognizes diverse VKD substrates through high-affinity propeptide binding, while substrates like osteocalcin utilize a secondary exosite to enhance interaction. GGCX employs a conserved dipeptide anchoring mechanism that ensures processive carboxylation of glutamate residues. GGCX undergoes allosteric conformational changes that enable coordinated binding of vitamin K and glutamate substrates, facilitating the catalytic process. Additionally, we reveal a bicarbonate-mediated CO₂ capture mechanism that is conserved across bacterial and eukaryotic species, suggesting that this strategy for CO₂ utilization is both ancient and universal. Our findings lay the foundation for developing targeted anticoagulant drugs and innovative enzymatic CO₂ fixation strategies.
External links	Nat Commun / PubMed:41290650 / PubMed Central
Methods	EM (single particle)
Resolution	2.41 - 3.46 Å
Structure data	62758 9l1y EMDB-62758, PDB-9l1y: Vitamin K-dependent gamma-carboxylase apo status Method: EM (single particle) / Resolution: 3.46 Å 62764 9l20 EMDB-62764, PDB-9l20: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with anisindione Method: EM (single particle) / Resolution: 2.82 Å 62765 9l21 EMDB-62765, PDB-9l21: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX Method: EM (single particle) / Resolution: 2.62 Å 62767 9l23 EMDB-62767, PDB-9l23: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Osteocalcin Method: EM (single particle) / Resolution: 2.62 Å 62768 9l24 EMDB-62768, PDB-9l24: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Matrix Gla protein Method: EM (single particle) / Resolution: 3.1 Å 62769 9l25 EMDB-62769, PDB-9l25: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla) Method: EM (single particle) / Resolution: 2.41 Å 62822 9l54 EMDB-62822, PDB-9l54: cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Vitamin K1 2,3-epoxide Method: EM (single particle) / Resolution: 3.04 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-CLR: CHOLESTEROL ChemComp-Y01: CHOLESTEROL HEMISUCCINATE PDB-1at0: 17-kDA fragment of hedgehog C-terminal autoprocessing domain ChemComp-PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipidYM ChemComp-BCT: BICARBONATE ION / pH bufferYM PDB-1avc: BOVINE ANNEXIN VI (CALCIUM-BOUND) ChemComp-CO2: CARBON DIOXIDE ChemComp-HOH: WATER PDB-1eil: 2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE
Source	homo sapiens (human)
Keywords	MEMBRANE PROTEIN / apo