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1j35

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Revision as of 01:53, 11 September 2015

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Structural highlights

1j35 is a 3 chain structure with sequence from Bos taurus and Protobothrops flavoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1iod, 1bj3, 1j34
Activity:	Coagulation factor IXa, with EC number 3.4.21.22
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[FA9_BOVIN] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa. [IXXB_PROFL] 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

Factor IX is an indispensable protein required in the blood coagulation cascade. It binds to the surface of phospholipid membrane by means of a gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we showed that physiological concentrations of Mg2+ ions affect the native conformation of the Gla domain and in doing so augment the biological activity of factor IXa and binding affinity with its binding protein even in the presence of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg2+-free structure. The results clearly suggest that Mg2+ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.

Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein.,Shikamoto Y, Morita T, Fujimoto Z, Mizuno H J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512^[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
↑ Shikamoto Y, Morita T, Fujimoto Z, Mizuno H. Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein. J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512 doi:10.1074/jbc.M300650200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1j35"

@@ Line 2: / Line 2: @@
 <StructureSection load='1j35' size='340' side='right' caption='[[1j35]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1j35]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J35 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J35 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1j35]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Protobothrops_flavoviridis Protobothrops flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J35 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J35 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1iod|1iod]], [[1bj3|1bj3]], [[1j34|1j34]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] </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=1j35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j35 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j35 RCSB], [http://www.ebi.ac.uk/pdbsum/1j35 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=1j35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j35 OCA], [http://pdbe.org/1j35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j35 RCSB], [http://www.ebi.ac.uk/pdbsum/1j35 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1j35" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 38: / Line 39: @@
 [[Category: Bos taurus]]
 [[Category: Coagulation factor IXa]]
-[[Category: Trimeresurus flavoviridis]]
+[[Category: Protobothrops flavoviridis]]
 [[Category: Fujimoto, Z]]
 [[Category: Mizuno, H]]

1j35

From Proteopedia

Revision as of 01:53, 11 September 2015

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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