PDBsum entry 2a2q

Hydrolase/blood clotting

PDB id: 2a2q

Contents

Protein chains

142 a.a. *

254 a.a. *

191 a.a. *

Ligands

GLC

FUC

PBZ

Metals

_CA ×6

_CL ×3

_MG ×3

_NA

_ZN ×2

Waters ×722

* Residue conservation analysis

PDB id:

2a2q

Name:

Hydrolase/blood clotting

Title:

Complex of active-site inhibited human coagulation factor viia with human soluble tissue factor in the presence of ca2+, mg2+, na+, and zn2+

Structure:

Coagulation factor vii. Chain: l. Fragment: light chain, residues 61-212. Synonym: serum prothrombin conversion accelerator, spca, proconvertin, eptacog alfa. Engineered: yes. Coagulation factor vii. Chain: h. Fragment: heavy chain, residues 213-466.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: f7. Expressed in: mesocricetus auratus. Expression_system_taxid: 10036. Expression_system_cell_line: bhk. Other_details: plasmid. Gene: f3.

Biol. unit:

Trimer (from PQS)

Resolution:

1.80Å R-factor: 0.198 R-free: 0.259

Authors:

S.P.Bajaj,M.Bajaj,A.E.Schmidt,K.Padmanabhan

Key ref:

S.P.Bajaj et al. (2006). 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. PubMed id: 16757484 DOI: 10.1074/jbc.M509971200

Date:

22-Jun-05 Release date: 04-Jul-06

Protein chain

P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens

Seq: 466 a.a.

Struc: 142 a.a.*

Protein chain

P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens

Seq: 466 a.a.

Struc: 254 a.a.

Protein chain

P13726  (TF_HUMAN) -  Tissue factor from Homo sapiens

Seq: 295 a.a.

Struc: 191 a.a.

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.21 - coagulation factor VIIa.
• Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

DOI no: 10.1074/jbc.M509971200

J Biol Chem 281:24873-24888 (2006)

PubMed id: 16757484

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.

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan.

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.

Selected figure(s)

Figure 2.
FIGURE 2. Conformation of the loop and positions of the Ca^2^+ and Mg^2^+ ions in the FVIIa Gla domain. A, superpositioning of the Gla domain in the presence of Ca^2+/Mg^2+ versus Ca^2+ (19). The C atoms used for superpositioning were residues 13L-46L. The Ca^2+/Mg^2+ structure is in blue and the Ca^2+ structure is in magenta. Phe^4, Leu^5, Gla6, Gla7, and Leu^8 are depicted for both structures. Ca^2+ (blue) and Mg^2+ (cyan) ions for the present structure as well as Ca^2+ ions (magenta) for the PDB code 1DAN (19) are shown as spheres. N represents the N terminus of the Gla domain of FVIIa. B, coordination of the Ca^2+ and Mg^2+ ions in the Gla domain of the Ca^2+/Mg^2+ structure. Electron density (2F[obs] - F[calc]) contoured at 1 of all nine Gla residues as well as that of Ca^2+ (magenta spheres), Mg^2+ (cyan spheres), and coordinating water molecules (red spheres)is shown. Coordination of Ca5 to O of Ala^1L and H-bonds between Gla6 and the NH[2] side chain of Arg^9L, Gla7, and NofPhe^4L, and a water molecule with O [1] of Gln^2L are indicated with dashed arrows. Black dashed lines depict all other coordinations and H-bonds. A stereo figure is given in the supplemental material as Fig. 1S.

Figure 5.
FIGURE 5. Ca^2^+ site in the EGF1 domain and location of the Zn^2^+ sites and their linkage to the protease domain Ca^2^+ site in FVIIa. A, Ca^2+ site in the EGF1 domain. Electron density (2F[obs] - F[calc]) contoured at 1 (gray) for Ca^2+ (magenta sphere) and two water molecules (red spheres) is shown. Electron density contoured at 5 for Ca^2+ is shown in blue. Note that in the presence of Ca^2+, Mg^2+ will not occupy this site. All eight coordination ligands (black dashed lines) are shown, and the residues labeled are those of the light chain of FVIIa. B, location of the Zn^2+ sites and their linkage to the protease domain Ca^2+ site. Electron density (2F[obs] - F[calc]) contoured at 1 (gray) of Zn^2+ (cyan spheres), Ca^2+ (magenta sphere), and water molecules (red spheres) is shown. The electron density contoured at 3 for Zn^2+ and Ca^2+ ions is shown in blue. Note the linkage between the Zn^2+ sites and the Ca^2+ site. The metal ion coordination to its ligands and H-bonds between water molecules is shown with black dotted lines. Residue numbering used in the figure is that of chymotrypsin.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 24873-24888) copyright 2006.

Figures were selected by an automated process.