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2ero

From Proteopedia

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Current revision

Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form)

Structural highlights

2ero is a 2 chain structure with sequence from Crotalus atrox. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VM3V1_CROAT Zinc metalloprotease that has fibrinogenolytic and hemorrhagic activities. It induces apoptosis in vascular endothelial cells (VEC), without degrading extracellular matrix (it cannot cleave collagen) or inhibiting adhesion of VEC. VAP1-induced apoptosis is inhibited by antibodies for integrin alpha-3, alpha-6, beta-1 and CD9. Apoptosis is accompanied by severe cell fragmentation, which is controlled by caspases.^[1] ^[2] ^[3] ^[4] ^[5]

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

ADAMs (a disintegrin and metalloproteinase) are sheddases possessing extracellular metalloproteinase/disintegrin/cysteine-rich (MDC) domains. ADAMs uniquely display both proteolytic and adhesive activities on the cell surface, however, most of their physiological targets and adhesion mechanisms remain unclear. Here for the first time, we reveal the ADAMs' MDC architecture and a potential target-binding site by solving crystal structures of VAP1, a snake venom homolog of mammalian ADAMs. The D-domain protrudes from the M-domain opposing the catalytic site and constituting a C-shaped arm with cores of Ca2+ ions. The disintegrin-loop, supposed to interact with integrins, is packed by the C-domain and inaccessible for protein binding. Instead, the hyper-variable region (HVR) in the C-domain, which has a novel fold stabilized by the strictly conserved disulfide bridges, constitutes a potential protein-protein adhesive interface. The HVR is located at the distal end of the arm and faces toward the catalytic site. The C-shaped structure implies interplay between the ADAMs' proteolytic and adhesive domains and suggests a molecular mechanism for ADAMs' target recognition for shedding.

Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold.,Takeda S, Igarashi T, Mori H, Araki S EMBO J. 2006 Jun 7;25(11):2388-96. Epub 2006 May 11. PMID:16688218^[6]

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

References

↑ Masuda S, Ohta T, Kaji K, Fox JW, Hayashi H, Araki S. cDNA cloning and characterization of vascular apoptosis-inducing protein 1. Biochem Biophys Res Commun. 2000 Nov 11;278(1):197-204. PMID:11071872 doi:10.1006/bbrc.2000.3770
↑ Araki S, Masuda S, Maeda H, Ying MJ, Hayashi H. Involvement of specific integrins in apoptosis induced by vascular apoptosis-inducing protein 1. Toxicon. 2002 May;40(5):535-42. PMID:11821125 doi:10.1016/s0041-0101(01)00249-5
↑ Maruyama J, Hayashi H, Miao J, Sawada H, Araki S. Severe cell fragmentation in the endothelial cell apoptosis induced by snake apoptosis toxin VAP1 is an apoptotic characteristic controlled by caspases. Toxicon. 2005 Jul;46(1):1-6. PMID:15922392 doi:10.1016/j.toxicon.2005.02.002
↑ Kikushima E, Nakamura S, Oshima Y, Shibuya T, Miao JY, Hayashi H, Nikai T, Araki S. Hemorrhagic activity of the vascular apoptosis-inducing proteins VAP1 and VAP2 from Crotalus atrox. Toxicon. 2008 Sep 15;52(4):589-93. PMID:18657564 doi:10.1016/j.toxicon.2008.06.027
↑ Masuda S, Araki S, Yamamoto T, Kaji K, Hayashi H. Purification of a vascular apoptosis-inducing factor from hemorrhagic snake venom. Biochem Biophys Res Commun. 1997 Jun 9;235(1):59-63. PMID:9196035 doi:10.1006/bbrc.1997.6728
↑ Takeda S, Igarashi T, Mori H, Araki S. Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold. EMBO J. 2006 Jun 7;25(11):2388-96. Epub 2006 May 11. PMID:16688218

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/2ero"

Categories: Crotalus atrox | Large Structures | Araki S | Igarashi T | Takeda S

@@ Line 1: / Line 1: @@
 ==Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form)==
-<StructureSection load='2ero' size='340' side='right' caption='[[2ero]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='2ero' size='340' side='right'caption='[[2ero]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ero]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ERO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ERO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ero]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ERO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ERO FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2erp|2erp]], [[2erq|2erq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2ero FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ero OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ero RCSB], [http://www.ebi.ac.uk/pdbsum/2ero PDBsum]</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=2ero FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ero OCA], [https://pdbe.org/2ero PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ero RCSB], [https://www.ebi.ac.uk/pdbsum/2ero PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ero ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VM3V1_CROAT VM3V1_CROAT] Zinc metalloprotease that has fibrinogenolytic and hemorrhagic activities. It induces apoptosis in vascular endothelial cells (VEC), without degrading extracellular matrix (it cannot cleave collagen) or inhibiting adhesion of VEC. VAP1-induced apoptosis is inhibited by antibodies for integrin alpha-3, alpha-6, beta-1 and CD9. Apoptosis is accompanied by severe cell fragmentation, which is controlled by caspases.<ref>PMID:11071872</ref> <ref>PMID:11821125</ref> <ref>PMID:15922392</ref> <ref>PMID:18657564</ref> <ref>PMID:9196035</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/2ero_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/2ero_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ero ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2ero" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 34: @@
 </StructureSection>
 [[Category: Crotalus atrox]]
-[[Category: Araki, S.]]
+[[Category: Large Structures]]
-[[Category: Igarashi, T.]]
+[[Category: Araki S]]
-[[Category: Takeda, S.]]
+[[Category: Igarashi T]]
-[[Category: Adam]]
+[[Category: Takeda S]]
-[[Category: Calcium-binding]]
-[[Category: Disintegrin]]
-[[Category: Mdc protein]]
-[[Category: Metalloprotease]]
-[[Category: Svmp]]
-[[Category: Toxin]]

2ero

From Proteopedia

Current revision

Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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