PDBsum entry 2h9e

Hydrolase/hydrolase inhibitor

PDB id: 2h9e

Contents

Protein chains

233 a.a. *

48 a.a. *

52 a.a. *

Ligands

DTY-ILE-ARG-LEU-LPD

PO4 ×6

ACT ×3

Metals

_NA

Waters ×258

* Residue conservation analysis

PDB id:

2h9e

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of fxa/selectide/napc2 ternary complex

Structure:

Coagulation factor x heavy chain. Chain: h. Fragment: catalytic domain. Coagulation factor x light chain. Chain: l. Fragment: egf-like 1 domain. Anti-coagulant protein c2. Chain: c. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Ancylostoma caninum. Dog hookworm. Organism_taxid: 29170. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes.

Resolution:

2.20Å R-factor: 0.222 R-free: 0.268

Authors:

M.T.Murakami,G.Geiger,A.Tulinsky,R.K.Arni

Key ref:

M.T.Murakami et al. (2007). Intermolecular Interactions and Characterization of the Novel Factor Xa Exosite Involved in Macromolecular Recognition and Inhibition: Crystal Structure of Human Gla-domainless Factor Xa Complexed with the Anticoagulant Protein NAPc2 from the Hematophagous Nematode Ancylostoma caninum. J Mol Biol, 366, 602-610. PubMed id: 17173931 DOI: 10.1016/j.jmb.2006.11.040

Date:

09-Jun-06 Release date: 13-Feb-07

Protein chain

P00742  (FA10_HUMAN) -  Coagulation factor X from Homo sapiens

Seq: 488 a.a.

Struc: 233 a.a.

Protein chain

P00742  (FA10_HUMAN) -  Coagulation factor X from Homo sapiens

Seq: 488 a.a.

Struc: 48 a.a.

Protein chain

Q16938  (Q16938_ANCCA) -  Anti-coagulant protein C2 (Fragment) from Ancylostoma caninum

Seq: 91 a.a.

Struc: 52 a.a.

Enzyme reactions

• Enzyme class: Chains H, L: E.C.3.4.21.6 - coagulation factor Xa.
• Reaction: Preferential cleavage: Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.

DOI no: 10.1016/j.jmb.2006.11.040

J Mol Biol 366:602-610 (2007)

PubMed id: 17173931

Intermolecular Interactions and Characterization of the Novel Factor Xa Exosite Involved in Macromolecular Recognition and Inhibition: Crystal Structure of Human Gla-domainless Factor Xa Complexed with the Anticoagulant Protein NAPc2 from the Hematophagous Nematode Ancylostoma caninum.

M.T.Murakami, J.Rios-Steiner, S.E.Weaver, A.Tulinsky, J.H.Geiger, R.K.Arni.

ABSTRACT

NAPc2, an anticoagulant protein from the hematophagous nematode Ancylostoma caninum evaluated in phase-II/IIa clinical trials, inhibits the extrinsic blood coagulation pathway by a two step mechanism, initially interacting with the hitherto uncharacterized factor Xa exosite involved in macromolecular recognition and subsequently inhibiting factor VIIa (K(i)=8.4 pM) of the factor VIIa/tissue factor complex. NAPc2 is highly flexible, becoming partially ordered and undergoing significant structural changes in the C terminus upon binding to the factor Xa exosite. In the crystal structure of the ternary factor Xa/NAPc2/selectide complex, the binding interface consists of an intermolecular antiparallel beta-sheet formed by the segment of the polypeptide chain consisting of residues 74-80 of NAPc2 with the residues 86-93 of factor Xa that is additional maintained by contacts between the short helical segment (residues 67-73) and a turn (residues 26-29) of NAPc2 with the short C-terminal helix of factor Xa (residues 233-243). This exosite is physiologically highly relevant for the recognition and inhibition of factor X/Xa by macromolecular substrates and provides a structural motif for the development of a new class of inhibitors for the treatment of deep vein thrombosis and angioplasty.

Selected figure(s)

Figure 2.
Figure 2. Overlays of the NAPc2 crystallographic structure (red) on (a) the NMR-derived average structure (gray); and (b) crystallographic structure of NAP5 (gray; J.R.S. and A.T., unpublished results). Figure 2. Overlays of the NAPc2 crystallographic structure (red) on (a) the NMR-derived average structure (gray); and (b) crystallographic structure of NAP5 (gray; J.R.S. and A.T., unpublished results).

Figure 3.
Figure 3. (a) Surface representation of the model of the complex TF (green), fVIIa (catalytic domain in pink and EGF1, EGF2 and Gla domains in yellow), fX (catalytic domain in gray and EGF1, EGF2 and Gla domains in blue). NAPc2 is in red (ribbon representation), yellow circle and arrow indicate the position of the insertion-loop containing the P1 (Arg44) residue. (b) Same as (a) but with the fXa re-positioned to permit the simultaneous binding of NAPc2 to the fXa exosite and the fVIIa active site. (c) Ribbon representation of the fXa-NAPc2 complex. The yellow circle indicates the antiparallel β-strand interactions between NAPc2 (red) and fXa (dark blue). (d) Surface charge of fVIIa with the modeled peptide fragment of the NAPc2 insertion-loop containing Arg44 in the active site cavity. Figure 3. (a) Surface representation of the model of the complex TF (green), fVIIa (catalytic domain in pink and EGF1, EGF2 and Gla domains in yellow), fX (catalytic domain in gray and EGF1, EGF2 and Gla domains in blue). NAPc2 is in red (ribbon representation), yellow circle and arrow indicate the position of the insertion-loop containing the P1 (Arg44) residue. (b) Same as (a) but with the fXa re-positioned to permit the simultaneous binding of NAPc2 to the fXa exosite and the fVIIa active site. (c) Ribbon representation of the fXa-NAPc2 complex. The yellow circle indicates the antiparallel β-strand interactions between NAPc2 (red) and fXa (dark blue). (d) Surface charge of fVIIa with the modeled peptide fragment of the NAPc2 insertion-loop containing Arg44 in the active site cavity.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 602-610) copyright 2007.

Figures were selected by an automated process.