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5yjs

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Structure of vicilin from Capsicum annuum

Structural highlights

5yjs is a 2 chain structure with sequence from Capsicum annuum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.16Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A452CSM5_CAPAN

Publication Abstract from PubMed

Proteins belonging to cupin superfamily are known to have critical and diverse physiological functions. However, 7S globulins family, which is also a part of cupin superfamily were undermined as only seed storage proteins. Structure determination of native protein - Vic_CAPAN from Capsicumannuum was carried out, and its physiological functions were explored after purifying the protein by ammonium sulfate precipitation followed by size exclusion chromatography. The crystal structure of vicilin determined at 2.16 A resolution revealed two monomers per asymmetric unit which are juxtaposed orthogonal with each other. Vic_CAPAN consists predominately of beta-sheets which folds to form a beta-barrel structure commonly called cupin fold. Each monomer of Vic_CAPAN consists of two cupin fold domains, N-terminal and C-terminal, which accommodate two different ligands. A bound ligand was identified at the C-terminal cupin fold in the site presumably conserved for metabolites in the crystal structure. The ligand was confirmed to be salicylic acid through mass spectrometric analysis. A copper binding site was further observed near the conserved ligand binding pocket, suggesting possible superoxide dismutase activity of Vic_CAPAN which was subsequently confirmed biochemically. Vicilins from other sources did not exhibit this activity indicating functional specificity of Vic_CAPAN. Discovery of bound salicylic acid, which is a known regulator of antioxidant pathway and revelation of superoxide dismutase activity suggest that Vic_CAPAN has important role during oxidative stress. As salicylic acid changes the redox state of cell, it may act as a downstream signal for various pathways involved in plant biotic and abiotic stress rescue.

Structure-guided identification of function: role of C. annuum vicilin during oxidative stress.,Shikhi M, Nair DT, Salunke DM Biochem J. 2018 Sep 4. pii: BCJ20180520. doi: 10.1042/BCJ20180520. PMID:30181145^[1]

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

References

↑ Shikhi M, Nair DT, Salunke DM. Structure-guided identification of function: role of C. annuum vicilin during oxidative stress. Biochem J. 2018 Sep 4. pii: BCJ20180520. doi: 10.1042/BCJ20180520. PMID:30181145 doi:http://dx.doi.org/10.1042/BCJ20180520

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yjs"

Categories: Capsicum annuum | Large Structures | Nair DT | Salunke DM | Shikhi M

@@ Line 3: / Line 3: @@
 <StructureSection load='5yjs' size='340' side='right'caption='[[5yjs]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yjs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Capsicum_annuum Capsicum annuum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YJS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YJS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yjs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Capsicum_annuum Capsicum annuum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YJS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</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]] 2.16&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yjs OCA], [http://pdbe.org/5yjs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yjs RCSB], [http://www.ebi.ac.uk/pdbsum/5yjs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yjs 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=5yjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yjs OCA], [https://pdbe.org/5yjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yjs RCSB], [https://www.ebi.ac.uk/pdbsum/5yjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yjs ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A452CSM5_CAPAN A0A452CSM5_CAPAN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 25: @@
 [[Category: Capsicum annuum]]
 [[Category: Large Structures]]
-[[Category: Nair, D T]]
+[[Category: Nair DT]]
-[[Category: Salunke, D M]]
+[[Category: Salunke DM]]
-[[Category: Shikhi, M]]
+[[Category: Shikhi M]]
-[[Category: 7s globulin]]
-[[Category: Binding pocket]]
-[[Category: Copper site]]
-[[Category: Cupin]]
-[[Category: Plant protein]]

5yjs

From Proteopedia

Current revision

Structure of vicilin from Capsicum annuum

Structural highlights

Function

Publication Abstract from PubMed

References

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