1vpi

From Proteopedia

(Difference between revisions)

Current revision

PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN

Structural highlights

1vpi is a 1 chain structure with sequence from Vipera ammodytes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.76Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2HA_VIPAE Heterodimer: postsynaptic neurotoxin.^[1] Monomer: Acidic phospholipase A2 homolog that is non-toxic.^[2]

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

The high resolution crystal structure of a natural PLA2 inhibitor has been determined by Patterson search methods. In the heterodimeric, neurotoxic complex, vipoxin, isolated from the venom of Bulgarian viper, PLA2 inhibitor represents the non-toxic subunit. The model was refined to a crystallographic R-factor of 15.5% for data between 6 and 1.76 A resolution. The packing of the inhibitor in the crystal reveals close contacts between the molecules, which are symmetry-related by the 2-fold axes of the lattice. These pairs associate as a crystallographic dimer, stabilized by a set of interactions, including van der Waals contacts between residues from symmetry-related pairs, denoted as the recognition site and the recognition surface. Residues Ph3, Trp31 and Tyr119 represent the recognition site of inhibitor which possibly fits to the hydrophobic wall of the target PLA2. The topology of the inhibitor represents the PLA2 type of folding: three long helices and a beta-hairpin. Superposition of the structure of the inhibitor shows an almost complete overlap with different mammalian and viper PLA2 in the backbone and in the position of the sidechains of the residues that belong to the active centre and the hydrophobic wall. A "lock and key" mechanism of recognition of its native PLA2 in gland cells and other toxic PLA2 in vitro has been suggested. The mechanism includes complementary "head to tail" interactions between the recognition site of the inhibitor and a recognition surface located on the hydrophobic wall of the target PLA2. Having a high spatial homology with the PLA2 family of enzymes but opposing their action, the inhibitor from vipoxin presents an example of a divergent evolution of an ancient PLA2. The presence of a space for binding calcium in the inhibitor is believed to be a rudiment and proof of a common origin with PLA2.

X-ray structure at 1.76 A resolution of a polypeptide phospholipase A2 inhibitor.,Devedjiev Y, Popov A, Atanasov B, Bartunik HD J Mol Biol. 1997 Feb 14;266(1):160-72. PMID:9054978^[3]

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

References

↑ Atanasov VN, Stoykova S, Goranova Y, Mitewa M, Petrova S. Acute toxicity of vipoxin and its components: is the acidic component an "inhibitor" of PLA2 toxicity? Interdiscip Toxicol. 2012 Dec;5(4):169-72. doi: 10.2478/v10102-012-0028-z. PMID:23554559 doi:http://dx.doi.org/10.2478/v10102-012-0028-z
↑ Atanasov VN, Stoykova S, Goranova Y, Mitewa M, Petrova S. Acute toxicity of vipoxin and its components: is the acidic component an "inhibitor" of PLA2 toxicity? Interdiscip Toxicol. 2012 Dec;5(4):169-72. doi: 10.2478/v10102-012-0028-z. PMID:23554559 doi:http://dx.doi.org/10.2478/v10102-012-0028-z
↑ Devedjiev Y, Popov A, Atanasov B, Bartunik HD. X-ray structure at 1.76 A resolution of a polypeptide phospholipase A2 inhibitor. J Mol Biol. 1997 Feb 14;266(1):160-72. PMID:9054978 doi:10.1006/jmbi.1996.0778

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/1vpi"

Categories: Large Structures | Vipera ammodytes | Devedjiev YD | Popov AN

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1vpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vipera_ammodytes Vipera ammodytes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VPI FirstGlance]. <br>
-</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=1vpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vpi OCA], [https://pdbe.org/1vpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vpi RCSB], [https://www.ebi.ac.uk/pdbsum/1vpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vpi ProSAT]</span></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]] 1.76&#8491;</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=1vpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vpi OCA], [https://pdbe.org/1vpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vpi RCSB], [https://www.ebi.ac.uk/pdbsum/1vpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vpi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PA2A_VIPAE PA2A_VIPAE]] Heterodimer: postsynaptic neurotoxin.<ref>PMID:23554559</ref>   Monomer: Acidic phospholipase A2 homolog that is non-toxic.<ref>PMID:23554559</ref>
+[https://www.uniprot.org/uniprot/PA2HA_VIPAE PA2HA_VIPAE] Heterodimer: postsynaptic neurotoxin.<ref>PMID:23554559</ref>   Monomer: Acidic phospholipase A2 homolog that is non-toxic.<ref>PMID:23554559</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vp/1vpi_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 36: / Line 37: @@
 [[Category: Large Structures]]
 [[Category: Vipera ammodytes]]
-[[Category: Devedjiev, Y D]]
+[[Category: Devedjiev YD]]
-[[Category: Popov, A N]]
+[[Category: Popov AN]]
-[[Category: Molecular evolution]]
-[[Category: Neurotoxin]]
-[[Category: Phospholipase a2 inhibitor]]
-[[Category: Recognition]]

1vpi

From Proteopedia

Current revision

PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox