2FIR

Crystal structure of DFPR-VIIa/sTF

2FIR の概要

• エントリーDOI: 10.2210/pdb2fir/pdb
• 関連するPDBエントリー: 1DAN 2A2Q 2AER 2B8O
• 関連するBIRD辞書のPRD_ID: PRD_000021
• 分子名称: Coagulation factor VII Light chain, ZINC ION, CHLORIDE ION, ... (12 entities in total)
• 機能のキーワード: factor viia, soluble tissue factor, oxyanion hole, serine protease, blood coagulation, blood clotting, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 69134.80

構造登録者

Bajaj, S.P.,Schmidt, A.E.,Padmanabhan, K.,Bajaj, M.S.,Prevost, D.,Schreuder, H. (登録日: 2005-12-30, 公開日: 2006-07-11, 最終更新日: 2024-12-25)

主引用文献

Bajaj, S.P.,Schmidt, A.E.,Agah, S.,Bajaj, M.S.,Padmanabhan, K.
High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor: Unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in factor VIIa
J.Biol.Chem., 281:24873-24888, 2006

PubMed Abstract: Factor VIIa (FVIIa) consists of a gamma-carboxyglutamic acid (Gla) domain, two epidermal growth factor-like domains, and a protease domain. FVIIa binds seven Ca(2+) ions in the Gla, one in the EGF1, and one in the protease domain. However, blood contains both Ca(2+) and Mg(2+), and the Ca(2+) sites in FVIIa that could be specifically occupied by Mg(2+) are unknown. Furthermore, FVIIa contains a Na(+) and two Zn(2+) sites, but ligands for these cations are undefined. We obtained p-aminobenzamidine-VIIa/soluble tissue factor (sTF) crystals under conditions containing Ca(2+), Mg(2+), Na(+), and Zn(2+). The crystal diffracted to 1.8A resolution, and the final structure has an R-factor of 19.8%. In this structure, the Gla domain has four Ca(2+) and three bound Mg(2+). The EGF1 domain contains one Ca(2+) site, and the protease domain contains one Ca(2+), one Na(+), and two Zn(2+) sites. (45)Ca(2+) binding in the presence/absence of Mg(2+) to FVIIa, Gla-domainless FVIIa, and prothrombin fragment 1 supports the crystal data. Furthermore, unlike in other serine proteases, the amide N of Gly(193) in FVIIa points away from the oxyanion hole in this structure. Importantly, the oxyanion hole is also absent in the benzamidine-FVIIa/sTF structure at 1.87A resolution. However, soaking benzamidine-FVIIa/sTF crystals with d-Phe-Pro-Arg-chloromethyl ketone results in benzamidine displacement, d-Phe-Pro-Arg incorporation, and oxyanion hole formation by a flip of the 192-193 peptide bond in FVIIa. Thus, it is the substrate and not the TF binding that induces oxyanion hole formation and functional active site geometry in FVIIa. Absence of oxyanion hole is unusual and has biologic implications for FVIIa macromolecular substrate specificity and catalysis.

PubMed: 16757484
DOI: 10.1074/jbc.M509971200

実験手法

X-RAY DIFFRACTION (2 Å)