1x2w

From Proteopedia

(Difference between revisions)

Revision as of 19:35, 25 December 2014

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

Structural highlights

1x2w is a 2 chain structure with sequence from Trimeresurus flavoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1x2t
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[IXB_TRIFL] When linked to subunit A of IX/X-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factors IX (F9) and factor X (10) in the presence of calcium with a 1 to 1 stoichiometry.^[1] ^[2] ^[3] When linked to subunit A of IX-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (but not to factor X) in the presence of calcium with a 1 to 1 stoichiometry.^[4] ^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Atoda H, Morita T. A novel blood coagulation factor IX/factor X-binding protein with anticoagulant activity from the venom of Trimeresurus flavoviridis (Habu snake): isolation and characterization. J Biochem. 1989 Nov;106(5):808-13. PMID:2613688
↑ Atoda H, Yoshida N, Ishikawa M, Morita T. Binding properties of the coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis. Eur J Biochem. 1994 Sep 1;224(2):703-8. PMID:7925387
↑ Atoda H, Ishikawa M, Yoshihara E, Sekiya F, Morita T. Blood coagulation factor IX-binding protein from the venom of Trimeresurus flavoviridis: purification and characterization. J Biochem. 1995 Nov;118(5):965-73. PMID:8749314
↑ Atoda H, Morita T. A novel blood coagulation factor IX/factor X-binding protein with anticoagulant activity from the venom of Trimeresurus flavoviridis (Habu snake): isolation and characterization. J Biochem. 1989 Nov;106(5):808-13. PMID:2613688
↑ Atoda H, Yoshida N, Ishikawa M, Morita T. Binding properties of the coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis. Eur J Biochem. 1994 Sep 1;224(2):703-8. PMID:7925387
↑ Atoda H, Ishikawa M, Yoshihara E, Sekiya F, Morita T. Blood coagulation factor IX-binding protein from the venom of Trimeresurus flavoviridis: purification and characterization. J Biochem. 1995 Nov;118(5):965-73. PMID:8749314
↑ 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. 2005 Oct 14;353(1):80-7. PMID:16165155 doi:10.1016/j.jmb.2005.08.018

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1x2w"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1x2w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X2W FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x2t|1x2t]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x2t|1x2t]]</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1x2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x2w RCSB], [http://www.ebi.ac.uk/pdbsum/1x2w PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1x2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x2w RCSB], [http://www.ebi.ac.uk/pdbsum/1x2w PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/IXB_TRIFL IXB_TRIFL]] When linked to subunit A of IX/X-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factors IX (F9) and factor X (10) in the presence of calcium with a 1 to 1 stoichiometry.<ref>PMID:2613688</ref> <ref>PMID:7925387</ref> <ref>PMID:8749314</ref>   When linked to subunit A of IX-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (but not to factor X) in the presence of calcium with a 1 to 1 stoichiometry.<ref>PMID:2613688</ref> <ref>PMID:7925387</ref> <ref>PMID:8749314</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 32: @@
 </StructureSection>
 [[Category: Trimeresurus flavoviridis]]
-[[Category: Fujimoto, Z.]]
+[[Category: Fujimoto, Z]]
-[[Category: Fukamizu, A.]]
+[[Category: Fukamizu, A]]
-[[Category: Mizuno, H.]]
+[[Category: Mizuno, H]]
-[[Category: Morita, T.]]
+[[Category: Morita, T]]
-[[Category: Suzuki, N.]]
+[[Category: Suzuki, N]]
 [[Category: C-type lectin-like protein]]
 [[Category: Domain swapping]]
 [[Category: Heterodimer]]
 [[Category: Protein binding]]

1x2w

From Proteopedia

Revision as of 19:35, 25 December 2014

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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