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1x2t

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Revision as of 13:39, 17 July 2019

Crystal Structure of Habu IX-bp at pH 6.5

Structural highlights

1x2t is a 4 chain structure with sequence from Bothrops flavoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1x2w
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SLA_PROFL] Anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (F9) (but not factor X) in the presence of calcium with a 1 to 1 stoichiometry.^[1] ^[2] [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.^[3] ^[4] ^[5] 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.^[6] ^[7] ^[8]

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^[9]

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

References

↑ 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
↑ 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
↑ 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/1x2t"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Habu IX-bp at pH 6.5==
-<StructureSection load='1x2t' size='340' side='right' caption='[[1x2t]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+<StructureSection load='1x2t' size='340' side='right'caption='[[1x2t]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1x2t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_flavoviridis Bothrops flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X2T FirstGlance]. <br>
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x2/1x2t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x2/1x2t_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bothrops flavoviridis]]
+[[Category: Large Structures]]
 [[Category: Fujimoto, Z]]
 [[Category: Fukamizu, A]]

1x2t

From Proteopedia

Revision as of 13:39, 17 July 2019

Crystal Structure of Habu IX-bp at pH 6.5

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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