3s9c: Difference between revisions

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==Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V==
==Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V==
<StructureSection load='3s9c' size='340' side='right' caption='[[3s9c]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3s9c' size='340' side='right'caption='[[3s9c]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3s9c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dabsi Dabsi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S9C FirstGlance]. <br>
<table><tr><td colspan='2'>[[3s9c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Daboia_siamensis Daboia siamensis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S9C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S9C FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3s9a|3s9a]], [[3s9b|3s9b]], [[3sbk|3sbk]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Snake_venom_factor_V_activator Snake venom factor V activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.95 3.4.21.95] </span></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=3s9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s9c OCA], [https://pdbe.org/3s9c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s9c RCSB], [https://www.ebi.ac.uk/pdbsum/3s9c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s9c ProSAT]</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=3s9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s9c OCA], [http://pdbe.org/3s9c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s9c RCSB], [http://www.ebi.ac.uk/pdbsum/3s9c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s9c ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/FA5_HUMAN FA5_HUMAN]] Defects in F5 are the cause of factor V deficiency (FA5D) [MIM:[http://omim.org/entry/227400 227400]]; also known as Owren parahemophilia. It is a hemorrhagic diastesis.<ref>PMID:10942390</ref> <ref>PMID:12393490</ref>  Defects in F5 are the cause of thrombophilia due to activated protein C resistance (THPH2) [MIM:[http://omim.org/entry/188055 188055]]. THPH2 is a hemostatic disorder due to defective degradation of factor Va by activated protein C. It is characterized by a poor anticoagulant response to activated protein C resulting in tendency to thrombosis.<ref>PMID:9454742</ref> <ref>PMID:11435304</ref> <ref>PMID:11858490</ref> <ref>PMID:14617013</ref> <ref>PMID:14695241</ref>  Defects in F5 are a cause of susceptibility to Budd-Chiari syndrome (BDCHS) [MIM:[http://omim.org/entry/600880 600880]]. A syndrome caused by obstruction of hepatic venous outflow involving either the hepatic veins or the terminal segment of the inferior vena cava. Obstructions are generally caused by thrombosis and lead to hepatic congestion and ischemic necrosis. Clinical manifestations observed in the majority of patients include hepatomegaly, right upper quadrant pain and abdominal ascites. Budd-Chiari syndrome is associated with a combination of disease states including primary myeloproliferative syndromes and thrombophilia due to factor V Leiden, protein C deficiency and antithrombin III deficiency. Budd-Chiari syndrome is a rare but typical complication in patients with polycythemia vera.  Defects in F5 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref>  Defects in F5 are associated with susceptibility to pregnancy loss, recurrent, type 1 (RPRGL1) [MIM:[http://omim.org/entry/614389 614389]]. RPRGL1 is a common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11018168</ref> 
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/VSPG_DABSI VSPG_DABSI]] Venom serine protease that selectively activates factor V (F5) in a calcium-independent manner. It cleaves the Arg(1545)-Ser(1546) linkage in the human factor V molecule. Induces the coagulation of mammalian plasma.<ref>PMID:3053712</ref> [[http://www.uniprot.org/uniprot/FA5_HUMAN FA5_HUMAN]] Central regulator of hemostasis. It serves as a critical cofactor for the prothrombinase activity of factor Xa that results in the activation of prothrombin to thrombin.
[https://www.uniprot.org/uniprot/VSPG_DABSI VSPG_DABSI] Venom serine protease that selectively activates factor V (F5) in a calcium-independent manner. It cleaves the Arg(1545)-Ser(1546) linkage in the human factor V molecule. Induces the coagulation of mammalian plasma.<ref>PMID:3053712</ref>  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
*[[Proteinase|Proteinase]]
*[[Proteinase 3D structures|Proteinase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dabsi]]
[[Category: Daboia siamensis]]
[[Category: Snake venom factor V activator]]
[[Category: Homo sapiens]]
[[Category: Ammar, Y Ben]]
[[Category: Large Structures]]
[[Category: Nakayama, D]]
[[Category: Ben Ammar Y]]
[[Category: Takeda, S]]
[[Category: Nakayama D]]
[[Category: Double six-stranded beta-barrel]]
[[Category: Takeda S]]
[[Category: Glycosylation]]
[[Category: Hydrolase]]
[[Category: Serine proteinase]]

Latest revision as of 20:23, 1 November 2023

Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor VRussell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V

Structural highlights

3s9c is a 2 chain structure with sequence from Daboia siamensis and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VSPG_DABSI Venom serine protease that selectively activates factor V (F5) in a calcium-independent manner. It cleaves the Arg(1545)-Ser(1546) linkage in the human factor V molecule. Induces the coagulation of mammalian plasma.[1]

Publication Abstract from PubMed

Russell's viper venom factor V (FV) activator (RVV-V) is a thrombin-like proteinase that specifically cleaves the Arg1545-Ser1546 bond of FV. Here we present the crystal structure of RVV-V in complex with the FV14 peptide (residues 1533-1546 of human FV) determined at 1.8A resolution. The structure reveals multiple interactions between RVV-V and the seven residues, Ile1539 (P(7))-Arg1545 (P(1)), of the cleaved substrate. Comparison with substrate-free structures reveals conformational changes of the RVV-V loops upon substrate binding, suggesting that the multiple interactions are mediated by an induced-fit mechanism. The results provide an explanation for the narrow specificity of RVV-V.

Structural basis of coagulation factor V recognition for cleavage by RVV-V.,Nakayama D, Ben Ammar Y, Miyata T, Takeda S FEBS Lett. 2011 Aug 23. PMID:21871889[2]

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

See Also

References

  1. ↑ Tokunaga F, Nagasawa K, Tamura S, Miyata T, Iwanaga S, Kisiel W. The factor V-activating enzyme (RVV-V) from Russell's viper venom. Identification of isoproteins RVV-V alpha, -V beta, and -V gamma and their complete amino acid sequences. J Biol Chem. 1988 Nov 25;263(33):17471-81. PMID:3053712
  2. ↑ Nakayama D, Ben Ammar Y, Miyata T, Takeda S. Structural basis of coagulation factor V recognition for cleavage by RVV-V. FEBS Lett. 2011 Aug 23. PMID:21871889 doi:10.1016/j.febslet.2011.08.022

3s9c, resolution 1.80Å

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