PDBsum entry 2p3f

Hydrolase

PDB id: 2p3f

Contents

Protein chains

235 a.a. *

51 a.a. *

74 a.a. *

Metals

_NA

Waters ×52

* Residue conservation analysis

PDB id:

2p3f

Name:

Hydrolase

Title:

Crystal structure of the factor xa/nap5 complex

Structure:

Coagulation factor x. Chain: h. Fragment: activated factor xa heavy chain domain. Synonym: stuart factor, stuart-prower factor. Coagulation factor x. Chain: l. Fragment: egf-like 2 domain. Synonym: stuart factor, stuart-prower factor. Anti-coagulant protein 5.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Ancylostoma caninum. Dog hookworm. Organism_taxid: 29170

Resolution:

3.10Å R-factor: 0.180 R-free: 0.280

Authors:

J.L.Rios-Steiner,M.T.Murakami,A.Tulinsky,R.K.Arni

Key ref:

J.L.Rios-Steiner et al. (2007). Active and exo-site inhibition of human factor Xa: structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum. J Mol Biol, 371, 774-786. PubMed id: 17588602 DOI: 10.1016/j.jmb.2007.05.042

Date:

08-Mar-07 Release date: 06-Nov-07

Protein chain

P00742  (FA10_HUMAN) -  Coagulation factor X from Homo sapiens

Seq: 488 a.a.

Struc: 235 a.a.

Protein chain

P00742  (FA10_HUMAN) -  Coagulation factor X from Homo sapiens

Seq: 488 a.a.

Struc: 51 a.a.

Protein chain

Q16940  (Q16940_ANCCA) -  Anti-coagulant protein 5 from Ancylostoma caninum

Seq: 100 a.a.

Struc: 74 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.2007.05.042

J Mol Biol 371:774-786 (2007)

PubMed id: 17588602

Active and exo-site inhibition of human factor Xa: structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum.

J.L.Rios-Steiner, M.T.Murakami, A.Tulinsky, R.K.Arni.

ABSTRACT

Hookworms are hematophagous nematodes capable of growth, development and subsistence in living host systems such as humans and other mammals. Approximately one billion, or one in six, people worldwide are infected by hookworms causing gastrointestinal blood loss and iron deficiency anemia. The hematophagous hookworm Ancylostoma caninum produces a family of small, disulfide-linked protein anticoagulants (75-84 amino acid residues). One of these nematode anticoagulant proteins, NAP5, inhibits the amidolytic activity of factor Xa (fXa) with K(i)=43 pM, and is the most potent natural fXa inhibitor identified thus far. The crystal structure of NAP5 bound at the active site of gamma-carboxyglutamic acid domainless factor Xa (des-fXa) has been determined at 3.1 A resolution, which indicates that Asp189 (fXa, S1 subsite) binds to Arg40 (NAP5, P1 site) in a mode similar to that of the BPTI/trypsin interaction. However, the hydroxyl group of Ser39 of NAP5 additionally forms a hydrogen bond (2.5 A) with His57 NE2 of the catalytic triad, replacing the hydrogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has not been observed before. Furthermore, the C-terminal extension of NAP5 surprisingly interacts with the fXa exosite of a symmetry-equivalent molecule forming a short intermolecular beta-strand as observed in the structure of the NAPc2/fXa complex. This indicates that NAP5 can bind to fXa at the active site, or the exosite, and to fX at the exosite. However, unlike NAPc2, NAP5 does not inhibit fVIIa of the fVIIa/TF complex.

Selected figure(s)

Figure 1.
Figure 1. Alignment of amino acid sequences of NAP5, NAP6 and NAPc2. Differences from NAP5 are in bold; disulfide bonds are shown as black lines; the conserved motif involved in exosite binding id boxed in dark gray; non-conserved motifs involved in the exosite binding boxed are in light gray; the NAP5 sequence is numbered consecutively.

Figure 2.
Figure 2. Stereoview of the superpositioning of C/E-1 on NAP5. A ribbon representation of NAP5 is in blue, the NAP5 disulfide bridges are numbered, reactive-site P1 residues are shown as yellow sticks (Arg40, NAP5; Leu31, C/E-1).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 774-786) copyright 2007.