1X2W

Crystal Structure of Apo-Habu IX-bp at pH 4.6

Summary for 1X2W

• Entry DOI: 10.2210/pdb1x2w/pdb
• Related: 1X2T
• Descriptor: Coagulation factor IX/X-binding protein A chain, Coagulation factor IX/factor X-binding protein B chain, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: heterodimer, domain swapping, c-type lectin-like protein, protein binding
• Biological source: Trimeresurus flavoviridis; More
• Cellular location: Secreted : Q7LZ71 P23807
• Total number of polymer chains: 2
• Total formula weight: 29412.71

Authors

Suzuki, N.,Fujimoto, Z.,Morita, T.,Fukamizu, A.,Mizuno, H. (deposition date: 2005-04-26, release date: 2005-10-04, Last modification date: 2024-10-16)

Primary citation

Suzuki, N.,Fujimoto, Z.,Morita, T.,Fukamizu, A.,Mizuno, H.
pH-Dependent Structural Changes at Ca(2+)-binding sites of Coagulation Factor IX-binding Protein
J.Mol.Biol., 353:80-87, 2005

PubMed 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.

PubMed: 16165155
DOI: 10.1016/j.jmb.2005.08.018

Experimental method

X-RAY DIFFRACTION (2.29 Å)