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2oqd

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Crystal Structure of BthTX-II

Structural highlights

2oqd is a 2 chain structure with sequence from Bothrops jararacussu. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.19Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2B2_BOTJR Snake venom phospholipase A2 (PLA2) that shows a moderate enzymatic activity. It induces indirect hemolytic, anticoagulant, and cytotoxic activities. In vivo, it induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. 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

A myotoxic Asp49-phospholipase A2 (Asp49-PLA2) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) was crystallized and the molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resembles the myotoxic Asp49-PLA2 PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA2S. Despite of this, BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA2 from B. jararacussu) and other Asp49-PLA2S. BthTX-II structure showed a severe distortion of calcium-binding loop leading to displacement of the C-terminal region. Tyr28 side chain, present in this region, is in an opposite position in relation to the same residue in the catalytic activity Asp49-PLA2S, making a hydrogen bond with the atom O delta 2 of the catalytically active Asp49, which should coordinate the calcium. This high distortion may also be confirmed by the inability of BthTX-II to bind Na+ ions at the Ca2+-binding loop, despite of the crystallization to have occurred in the presence of this ion. In contrast, other Asp49-PLA2S which are able to bind Ca2+ ions are also able to bind Na+ ions at this loop. The comparison with other catalytic, non-catalytic and inhibited PLA2S indicates that the BthTX-II is not able to bind calcium ions; consequently, we suggest that its low catalytic function is based on an alternative way compared with other PLA2S.

Crystal structure of a myotoxic Asp49-phospholipase A2 with low catalytic activity: Insights into Ca2+-independent catalytic mechanism.,Correa LC, Marchi-Salvador DP, Cintra AC, Sampaio SV, Soares AM, Fontes MR Biochim Biophys Acta. 2008 Apr;1784(4):591-9. Epub 2008 Jan 26. PMID:18261474^[3]

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

References

↑ Pereira MF, Novello JC, Cintra AC, Giglio JR, Landucci ET, Oliveira B, Marangoni S. The amino acid sequence of bothropstoxin-II, an Asp-49 myotoxin from Bothrops jararacussu (Jararacucu) venom with low phospholipase A2 activity. J Protein Chem. 1998 May;17(4):381-6. PMID:9619591
↑ Andriao-Escarso SH, Soares AM, Rodrigues VM, Angulo Y, Diaz C, Lomonte B, Gutierrez JM, Giglio JR. Myotoxic phospholipases A(2) in bothrops snake venoms: effect of chemical modifications on the enzymatic and pharmacological properties of bothropstoxins from Bothrops jararacussu. Biochimie. 2000 Aug;82(8):755-63. PMID:11018293
↑ Correa LC, Marchi-Salvador DP, Cintra AC, Sampaio SV, Soares AM, Fontes MR. Crystal structure of a myotoxic Asp49-phospholipase A2 with low catalytic activity: Insights into Ca2+-independent catalytic mechanism. Biochim Biophys Acta. 2008 Apr;1784(4):591-9. Epub 2008 Jan 26. PMID:18261474 doi:10.1016/j.bbapap.2008.01.007

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/2oqd"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of BthTX-II==
-<StructureSection load='2oqd' size='340' side='right' caption='[[2oqd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
+<StructureSection load='2oqd' size='340' side='right'caption='[[2oqd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2oqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OQD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2oqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OQD FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gmz|1gmz]], [[1u73|1u73]], [[1pao|1pao]]</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]] 2.19&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oqd OCA], [https://pdbe.org/2oqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oqd RCSB], [https://www.ebi.ac.uk/pdbsum/2oqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oqd 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=2oqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oqd OCA], [http://pdbe.org/2oqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oqd RCSB], [http://www.ebi.ac.uk/pdbsum/2oqd PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PA2B2_BOTJR PA2B2_BOTJR]] Snake venom phospholipase A2 (PLA2) that shows a moderate enzymatic activity. It induces indirect hemolytic, anticoagulant, and cytotoxic activities. In vivo, it induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:9619591</ref> <ref>PMID:11018293</ref>
+[https://www.uniprot.org/uniprot/PA2B2_BOTJR PA2B2_BOTJR] Snake venom phospholipase A2 (PLA2) that shows a moderate enzymatic activity. It induces indirect hemolytic, anticoagulant, and cytotoxic activities. In vivo, it induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:9619591</ref> <ref>PMID:11018293</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/oq/2oqd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/2oqd_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=2oqd ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[Phospholipase A2|Phospholipase A2]]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 36: @@
 </StructureSection>
 [[Category: Bothrops jararacussu]]
-[[Category: Cintra, A C.O]]
+[[Category: Large Structures]]
-[[Category: Correa, L C]]
+[[Category: Cintra ACO]]
-[[Category: Fontes, M R.M]]
+[[Category: Correa LC]]
-[[Category: Marchi-Salvador, D P]]
+[[Category: Fontes MRM]]
-[[Category: Soares, A M]]
+[[Category: Marchi-Salvador DP]]
-[[Category: Asp49-phospholipase a2]]
+[[Category: Soares AM]]
-[[Category: Bothropstoxin ii]]
-[[Category: Bthtx-ii]]
-[[Category: Hydrolase]]

2oqd

From Proteopedia

Current revision

Crystal Structure of BthTX-II

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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