3bjw

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of ecarpholin S complexed with suramin

Structural highlights

3bjw is a 8 chain structure with sequence from Echis carinatus. This structure supersedes the now removed PDB entry 2qhg. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PA2HS_ECHCA

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

Phospholipase A(2) (PLA(2)), a common toxic component of snake venom, has been implicated in various pharmacological effects. Ecarpholin S, isolated from the venom of the snake Echis carinatus sochureki, is a phospholipase A(2) (PLA(2)) belonging to the Ser(49)-PLA(2) subgroup. It has been characterized as having low enzymatic but potent myotoxic activities. The crystal structures of native ecarpholin S and its complexes with lauric acid, and its inhibitor suramin, were elucidated. This is the first report of the structure of a member of the Ser(49)-PLA(2) subgroup. We also examined interactions of ecarpholin S with phosphatidylglycerol and lauric acid, using surface plasmon resonance, and of suramin with isothermal titration calorimetry. Most Ca(2+)-dependent PLA(2) enzymes have Asp in position 49, which plays a crucial role in Ca(2+) binding. The three-dimensional structure of ecarpholin S reveals a unique conformation of the Ca(2+)-binding loop that is not favorable for Ca(2+) coordination. Furthermore, the endogenously bound fatty acid (lauric acid) in the hydrophobic channel may also interrupt the catalytic cycle. These two observations may account for the low enzymatic activity of ecarpholin S, despite full retention of the catalytic machinery. These observations may also be applicable to other non-Asp(49)-PLA(2) enzymes. The interaction of suramin in its complex with ecarpholin S is quite different from that reported for the Lys(49)-PLA(2)/suramin complex(,) where the interfacial recognition face (i-face), C-terminal region, and N-terminal region of ecarpholin S play important roles. This study provides significant structural and functional insights into the myotoxic activity of ecarpholin S and, in general, of non-Asp(49)-PLA(2) enzymes.

Structural characterization of myotoxic ecarpholin S from Echis carinatus venom.,Zhou X, Tan TC, Valiyaveettil S, Go ML, Kini RM, Velazquez-Campoy A, Sivaraman J Biophys J. 2008 Oct;95(7):3366-80. Epub 2008 Jun 27. PMID:18586854^[1]

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

References

↑ Zhou X, Tan TC, Valiyaveettil S, Go ML, Kini RM, Velazquez-Campoy A, Sivaraman J. Structural characterization of myotoxic ecarpholin S from Echis carinatus venom. Biophys J. 2008 Oct;95(7):3366-80. Epub 2008 Jun 27. PMID:18586854 doi:10.1529/biophysj.107.117747

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/3bjw"

Categories: Echis carinatus | Large Structures | Sivaraman J | Zhou X

@@ Line 1: / Line 1: @@
 ==Crystal Structure of ecarpholin S complexed with suramin==
-<StructureSection load='3bjw' size='340' side='right' caption='[[3bjw]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3bjw' size='340' side='right'caption='[[3bjw]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bjw]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qhg 2qhg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BJW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bjw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qhg 2qhg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</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]] 2.3&#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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</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=3bjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bjw RCSB], [http://www.ebi.ac.uk/pdbsum/3bjw 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=3bjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjw OCA], [https://pdbe.org/3bjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bjw RCSB], [https://www.ebi.ac.uk/pdbsum/3bjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjw ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2HS_ECHCA PA2HS_ECHCA]
 == 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/bj/3bjw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/3bjw_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=3bjw 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 3bjw" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Phospholipase A2|Phospholipase A2]]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
 == References ==
 <references/>
@@ Line 33: / Line 37: @@
 </StructureSection>
 [[Category: Echis carinatus]]
-[[Category: Sivaraman, J]]
+[[Category: Large Structures]]
-[[Category: Zhou, X]]
+[[Category: Sivaraman J]]
-[[Category: Complex]]
+[[Category: Zhou X]]
-[[Category: Hydrolase]]
-[[Category: Lipid degradation]]
-[[Category: Metal-binding]]
-[[Category: Phospholipase a2]]
-[[Category: Secreted]]
-[[Category: Ser49]]
-[[Category: Snake venom]]
-[[Category: Suramin]]
-[[Category: Toxin]]

3bjw

From Proteopedia

Current revision

Crystal Structure of ecarpholin S complexed with suramin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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