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| | ==STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION== | | ==STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION== |
| - | <StructureSection load='1jia' size='340' side='right' caption='[[1jia]], [[Resolution|resolution]] 2.13Å' scene=''> | + | <StructureSection load='1jia' size='340' side='right'caption='[[1jia]], [[Resolution|resolution]] 2.13Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1jia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agkistrodon_halys Agkistrodon halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JIA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1jia]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloydius_halys Gloydius halys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JIA 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></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]] 2.13Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></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></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=1jia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jia OCA], [http://pdbe.org/1jia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jia RCSB], [http://www.ebi.ac.uk/pdbsum/1jia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jia ProSAT]</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=1jia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jia OCA], [https://pdbe.org/1jia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jia RCSB], [https://www.ebi.ac.uk/pdbsum/1jia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jia ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PA2BB_GLOHA PA2BB_GLOHA]] Snake venom phospholipase A2 (PLA2) that shows potent hemolytic activity, and exhibits medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 90 nM). It is one of the few phospholipases A2 capable of hydrolyzing the phospholipids of E.coli membranes in the presence of a bactericidal/permeability-increasing protein (BPI) of neutrophils. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:10728829</ref> | + | [https://www.uniprot.org/uniprot/PA2BB_GLOHA PA2BB_GLOHA] Snake venom phospholipase A2 (PLA2) that shows potent hemolytic activity, and exhibits medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 90 nM). It is one of the few phospholipases A2 capable of hydrolyzing the phospholipids of E.coli membranes in the presence of a bactericidal/permeability-increasing protein (BPI) of neutrophils. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:10728829</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1jia_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1jia_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[Phospholipase A2|Phospholipase A2]] | + | *[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Agkistrodon halys]] | + | [[Category: Gloydius halys]] |
| - | [[Category: Lin, Z]] | + | [[Category: Large Structures]] |
| - | [[Category: Zhao, K]] | + | [[Category: Lin Z]] |
| - | [[Category: Agkistrodon halys pallas crystal structure]] | + | [[Category: Zhao K]] |
| - | [[Category: Phospholipase]]
| + | |
| - | [[Category: Phospholipase a2]]
| + | |
| Structural highlights
Function
PA2BB_GLOHA Snake venom phospholipase A2 (PLA2) that shows potent hemolytic activity, and exhibits medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 90 nM). It is one of the few phospholipases A2 capable of hydrolyzing the phospholipids of E.coli membranes in the presence of a bactericidal/permeability-increasing protein (BPI) of neutrophils. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.[1] [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 basic phospholipase A2 isolated from the venom of Agkistrodon halys Pallas (Agkistrodon blomhoffii Brevicaudus) is a hemolytic toxin and one of the few PLA2's capable of hydrolyzing the phospholipids of E. coli membranes in the presence of a bactericidal/permeability-increasing protein (BPI) of neutrophils. The crystal structure has been determined and refined at 2.13 A to an R factor of 16.5% (F > 3sigma) with excellent stereochemistry. A superposition of the two molecules in the asymmetric unit gives an r. m.s. deviation of 0.326 A for all Calpha atoms. The refined structure allowed a detailed comparison with other PLA2 species of known structures. The overall architecture is similar to those of other PLA2's with a few significant differences. One of which is in the region connecting the N-terminal helix and the Ca2+-binding loop. Unexpectedly, the conformation of the peptide plane Cys29-Gly30 in the Ca2+-binding loop is very different to that of other PLA2's. The amide NH of Gly30 does not point toward the proposed site for stabilization of the tetrahedral intermediate oxyanion of the substrate analogue. The structure includes four residues which occur less frequently in other PLA2's. His1, Arg6 and Trp70 located at the interfacial recognition site may play an important role in the interaction with aggregated substrates, while Trp77 contributes to the hydrophobic interactions between the beta-wing and the main body of the molecule. This structure analysis reveals that two clusters of basic residues are located at or near the interfacial recognition site, forming an asymmetric positively charge distribution. In contrast to the acidic isoform, the present enzyme is a dimer in the crystalline state. The special phospholipid hydrolysis behaviors are discussed in the light of the structure determined.
Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution.,Zhao K, Song S, Lin Z, Zhou Y Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):510-21. PMID:9761847[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Faure G, Gowda VT, Maroun RC. Characterization of a human coagulation factor Xa-binding site on Viperidae snake venom phospholipases A2 by affinity binding studies and molecular bioinformatics. BMC Struct Biol. 2007 Dec 6;7:82. PMID:18062812 doi:http://dx.doi.org/10.1186/1472-6807-7-82
- ↑ Zhao K, Zhou Y, Lin Z. Structure of basic phospholipase A2 from Agkistrodon halys Pallas: implications for its association, hemolytic and anticoagulant activities. Toxicon. 2000 Jul;38(7):901-16. PMID:10728829
- ↑ Zhao K, Song S, Lin Z, Zhou Y. Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution. Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):510-21. PMID:9761847
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