This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2qhd

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of ecarpholin S (ser49-PLA2) complexed with fatty acid

Structural highlights

2qhd is a 2 chain structure with sequence from Echis carinatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
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/2qhd"

@@ Line 1: / Line 1: @@
 ==Crystal structure of ecarpholin S (ser49-PLA2) complexed with fatty acid==
-<StructureSection load='2qhd' size='340' side='right' caption='[[2qhd]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='2qhd' size='340' side='right'caption='[[2qhd]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qhd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QHD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qhd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Echis_carinatus Echis carinatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QHD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAO:LAURIC+ACID'>DAO</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qhe|2qhe]], [[2qhg|2qhg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene></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=2qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qhd OCA], [https://pdbe.org/2qhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qhd RCSB], [https://www.ebi.ac.uk/pdbsum/2qhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qhd 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=2qhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qhd OCA], [http://pdbe.org/2qhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qhd RCSB], [http://www.ebi.ac.uk/pdbsum/2qhd PDBsum]</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/qh/2qhd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qh/2qhd_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=2qhd ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Phospholipase A2|Phospholipase A2]]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 37: @@
 </StructureSection>
 [[Category: Echis carinatus]]
-[[Category: Go, M L]]
+[[Category: Large Structures]]
-[[Category: Kini, R M]]
+[[Category: Go ML]]
-[[Category: Sivaraman, J]]
+[[Category: Kini RM]]
-[[Category: Tan, T C]]
+[[Category: Sivaraman J]]
-[[Category: Valiyaveettil, S]]
+[[Category: Tan TC]]
-[[Category: Zhou, X]]
+[[Category: Valiyaveettil S]]
-[[Category: Beta sheet]]
+[[Category: Zhou X]]
-[[Category: Hydrolase]]
-[[Category: Protein-ligand complex]]
-[[Category: Three helice]]

2qhd

From Proteopedia

Current revision

Crystal structure of ecarpholin S (ser49-PLA2) complexed with fatty acid

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