PDBsum entry 1x2w

Protein binding

PDB id: 1x2w

Contents

Protein chains

129 a.a. *

123 a.a. *

Ligands

SO4

Metals

_CL

_RB ×2

Waters ×323

* Residue conservation analysis

PDB id:

1x2w

Name:

Protein binding

Title:

Crystal structure of apo-habu ix-bp at ph 4.6

Structure:

Coagulation factor ix/x-binding protein a chain. Chain: a. Coagulation factor ix/factor x-binding protein b chain. Chain: b. Synonym: ix/x-bp

Source:

Trimeresurus flavoviridis. Organism_taxid: 88087. Secretion: venom. Secretion: venom

Biol. unit:

Dimer (from PQS)

Resolution:

2.29Å R-factor: 0.214 R-free: 0.280

Authors:

N.Suzuki,Z.Fujimoto,T.Morita,A.Fukamizu,H.Mizuno

Key ref:

N.Suzuki et al. (2005). pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein. J Mol Biol, 353, 80-87. PubMed id: 16165155 DOI: 10.1016/j.jmb.2005.08.018

Date:

26-Apr-05 Release date: 04-Oct-05

Protein chain

Q7LZ71  (SLA_PROFL) -  Snaclec coagulation factor IX-binding protein subunit A from Protobothrops flavoviridis

Seq: 129 a.a.

Struc: 129 a.a.

Protein chain

P23807  (SL9B_PROFL) -  Snaclec coagulation factor IX/factor X-binding protein subunit B from Protobothrops flavoviridis

Seq: 146 a.a.

Struc: 123 a.a.

DOI no: 10.1016/j.jmb.2005.08.018

J Mol Biol 353:80-87 (2005)

PubMed id: 16165155

pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein.

N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno.

ABSTRACT

Coagulation factor IX-binding protein, isolated from Trimeresurus flavoviridis (IX-bp), is a C-type lectin-like protein. It is an anticoagulant consisting of homologous subunits, A and B. Each subunit has a Ca(2+)-binding site with a unique affinity (K(d) values of 14muM and 130muM at pH 7.5). These binding characteristics are pH-dependent and, under acidic conditions, the Ca(2+) binding of the low-affinity site was reduced considerably. In order to identify which site has high affinity and to investigate the pH-dependent Ca(2+) release mechanism, we have determined the crystal structures of IX-bp at pH 6.5 and pH 4.6 (apo form), and compared the Ca(2+)-binding sites with each other and with those of the solved structures under alkaline conditions; pH 7.8 and pH 8.0 (complexed form). At pH 6.5, Glu43 in the Ca(2+)-binding site of subunit A displayed two conformations. One (minor) is that in the alkaline state, and the other (major) is that at pH 4.6. However, the corresponding Gln43 residue of subunit B is in only a single conformation, which is almost identical with that in the alkaline state. At pH 4.6, Glu43 of subunit A adopts a conformation similar to that of the major conformer observed at pH 6.5, while Gln43 of subunit B assumes a new conformation, and both Ca(2+) positions are occupied by water molecules. These results showed that Glu43 of subunit A is much more sensitive to protonation than Gln43 of subunit B, and the conformational change of Glu43 occurs around pH6.5, which may correspond to the step of Ca(2+) release.

Selected figure(s)

Figure 2.
Figure 2. Stereoviews of ball-and stick models of the Ca^2+-binding sites of (a) subunit A and (b) subunit B. The models at pH 8.0, pH 6.5 and pH 4.6 are shown in cyan, orange and magenta, respectively. Dotted lines in grey and green indicate Ca^2+ coordination and hydrogen bonds, respectively.

Figure 3.
Figure 3. Close-up views of pH-dependent conformational changes of (a) GluA43 and (b) GlnB43 coordinating to the Ca^2+. Conformational changes are shown by the rotation of torsion angles. The models at pH 8.0, pH 6.5 and pH 4.6 are shown in cyan, orange and magenta, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 80-87) copyright 2005.

Figures were selected by an automated process.