1x2t
From Proteopedia
(New page: 200px<br /><applet load="1x2t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1x2t, resolution 1.72Å" /> '''Crystal Structure of...) |
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| - | [[Image:1x2t.gif|left|200px]]<br /><applet load="1x2t" size=" | + | [[Image:1x2t.gif|left|200px]]<br /><applet load="1x2t" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1x2t, resolution 1.72Å" /> | caption="1x2t, resolution 1.72Å" /> | ||
'''Crystal Structure of Habu IX-bp at pH 6.5'''<br /> | '''Crystal Structure of Habu IX-bp at pH 6.5'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Coagulation factor IX-binding protein, isolated from Trimeresurus | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1X2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis] with CA and 1PE as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1X2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=1PE:'>1PE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X2T OCA]. |
==Reference== | ==Reference== | ||
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[[Category: heterodimer]] | [[Category: heterodimer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:50:31 2008'' |
Revision as of 13:50, 21 February 2008
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Crystal Structure of Habu IX-bp at pH 6.5
Overview
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.
About this Structure
1X2T is a Protein complex structure of sequences from Trimeresurus flavoviridis with and as ligands. Full crystallographic information is available from OCA.
Reference
pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein., Suzuki N, Fujimoto Z, Morita T, Fukamizu A, Mizuno H, J Mol Biol. 2005 Oct 14;353(1):80-7. PMID:16165155
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