3JTC

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins

Summary for 3JTC

• Entry DOI: 10.2210/pdb3jtc/pdb
• Descriptor: Endothelial protein C receptor, Vitamin K-dependent protein C, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: gla (gamma-carboxyglutamic acid) residues, phospholipid binding groove, ca ion binding, blood clotting, blood coagulation, disulfide bond, glycoprotein, membrane, receptor, transmembrane, cleavage on pair of basic residues, disease mutation, egf-like domain, gamma-carboxyglutamic acid, hydrolase, hydroxylation, protease, serine protease, thrombophilia, zymogen
• Biological source: HOMO SAPIENS (human); More
• Total number of polymer chains: 4
• Total formula weight: 56105.27

Authors

Bajaj, S.P.,Vadivel, K.,Agah, S.,Cascio, D.,Krishnaswamy, S.,Esmon, C.,Padmanabhan, K. (deposition date: 2009-09-11, release date: 2011-04-06, Last modification date: 2025-03-26)

Primary citation

Vadivel, K.,Agah, S.,Messer, A.S.,Cascio, D.,Bajaj, M.S.,Krishnaswamy, S.,Esmon, C.T.,Padmanabhan, K.,Bajaj, S.P.
Structural and Functional Studies of gamma-Carboxyglutamic Acid Domains of Factor VIIa and Activated Protein C: Role of Magnesium at Physiological Calcium.
J.Mol.Biol., 425:1961-1981, 2013

PubMed Abstract: Crystal structures of factor (F) VIIa/soluble tissue factor (TF), obtained under high Mg(2+) (50mM Mg(2+)/5mM Ca(2+)), have three of seven Ca(2+) sites in the γ-carboxyglutamic acid (Gla) domain replaced by Mg(2+) at positions 1, 4, and 7. We now report structures under low Mg(2+) (2.5mM Mg(2+)/5mM Ca(2+)) as well as under high Ca(2+) (5mM Mg(2+)/45 mM Ca(2+)). Under low Mg(2+), four Ca(2+) and three Mg(2+) occupy the same positions as in high-Mg(2+) structures. Conversely, under low Mg(2+), reexamination of the structure of Gla domain of activated Protein C (APC) complexed with soluble endothelial Protein C receptor (sEPCR) has position 4 occupied by Ca(2+) and positions 1 and 7 by Mg(2+). Nonetheless, in direct binding experiments, Mg(2+) replaced three Ca(2+) sites in the unliganded Protein C or APC. Further, the high-Ca(2+) condition was necessary to replace Mg4 in the FVIIa/soluble TF structure. In biological studies, Mg(2+) enhanced phospholipid binding to FVIIa and APC at physiological Ca(2+). Additionally, Mg(2+) potentiated phospholipid-dependent activations of FIX and FX by FVIIa/TF and inactivation of activated factor V by APC. Since APC and FVIIa bind to sEPCR involving similar interactions, we conclude that under the low-Mg(2+) condition, sEPCR binding to APC-Gla (or FVIIa-Gla) replaces Mg4 by Ca4 with an attendant conformational change in the Gla domain ω-loop. Moreover, since phospholipid and sEPCR bind to FVIIa or APC via the ω-loop, we predict that phospholipid binding also induces the functional Ca4 conformation in this loop. Cumulatively, the data illustrate that Mg(2+) and Ca(2+) act in concert to promote coagulation and anticoagulation.

PubMed: 23454357
DOI: 10.1016/j.jmb.2013.02.017

Experimental method

X-RAY DIFFRACTION (1.6 Å)