6mv4: Difference between revisions
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<StructureSection load='6mv4' size='340' side='right'caption='[[6mv4]], [[Resolution|resolution]] 1.37Å' scene=''> | <StructureSection load='6mv4' size='340' side='right'caption='[[6mv4]], [[Resolution|resolution]] 1.37Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6mv4]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6mv4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MV4 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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.37Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PBZ:P-AMINO+BENZAMIDINE'>PBZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6mv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mv4 OCA], [https://pdbe.org/6mv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mv4 RCSB], [https://www.ebi.ac.uk/pdbsum/6mv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mv4 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Disease == | == Disease == | ||
[ | [https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[https://omim.org/entry/306900 306900]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref> Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[https://omim.org/entry/300807 300807]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] 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. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6mv4" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6mv4" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Factor IX 3D structures|Factor IX 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bajaj | [[Category: Bajaj SP]] | ||
[[Category: Liesum | [[Category: Liesum A]] | ||
[[Category: Schreuder | [[Category: Schreuder HA]] | ||
[[Category: Vadivel | [[Category: Vadivel K]] | ||
Latest revision as of 09:39, 11 October 2023
CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXaCRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa
Structural highlights
DiseaseFA9_HUMAN Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:306900; also known as Christmas disease.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:300807. A hemostatic disorder characterized by a tendency to thrombosis.[37] FunctionFA9_HUMAN 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. Publication Abstract from PubMedBACKGROUND: Activated coagulation factor IX (FIXa) consists of a gamma-carboxyglutamic acid domain, two epidermal growth factor-like (EGF) domains and C-terminal protease domain. Consensus sequence and biochemical data support the existence of Na(+) -site in FIXa protease domain. However, soaking experiments or crystals grown in high concentration of ammonium sulfate did not reveal Na(+) -site in wild-type or mutant FIXa EGF2/protease domain structure. OBJECTIVE: Determine structure of FIXa EGF2/protease domain in presence of Na(+) ; perform molecular dynamics (MD) simulations to explore the role of Na(+) in stabilizing FIXa structure. METHODS: Crystallography, MD simulations and modeling heparin binding to FIXa. RESULTS: Crystal structure at 1.37 A resolution revealed that Na(+) is coordinated to carbonyl groups of residues 184A, 185, 221A and 224 in FIXa protease domain. Na(+) -site in FIXa is similar to that of FXa and is linked to Asp189 S1-site. In MD simulations, Na(+) reduced fluctuations in residues 217-225 (Na(+) -loop) and 70-80 (Ca(2+) -loop), whereas Ca(2+) reduced fluctuations only in residues of the Ca(2+) -loop. Ca(2+) and Na(+) together reduced fluctuations in residues of the Ca(2+) - and Na(+) -loops (residues 70-80, 183-194 and 217-225). Moreover, we observed four sulfate ions that make salt bridges with FIXa protease domain Arg/Lys residues, which have been implicated in heparin binding. Based upon locations of the sulfate ions, we modeled heparin binding to FIXa, which is similar to the heparin binding in thrombin. CONCLUSIONS: FIXa Na(+) -site in association with Ca(2+) contributes to stabilization of the FIXa protease domain. The heparin binding mode in FIXa is similar to that in thrombin. This article is protected by copyright. All rights reserved. Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study.,Vadivel K, Schreuder HA, Liesum A, Schmidt AE, Goldsmith G, Bajaj SP J Thromb Haemost. 2019 Feb 6. doi: 10.1111/jth.14401. PMID:30725510[38] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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