6l4c: Difference between revisions

Latest revision as of 10:51, 22 November 2023

Crystal structure of vicilin from Corylus avellana (Hazelnut)

Structural highlights

6l4c is a 3 chain structure with sequence from Corylus avellana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.191Å
Ligands:	CU
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VCL_CORAV Seed storage protein (PubMed:15233621, PubMed:19006093, PubMed:21563837, PubMed:21735061, PubMed:22966848, PubMed:22616776, PubMed:22812192, PubMed:23411333, Ref.12, PubMed:24577577, PubMed:25209075). Does not have superoxide dismutase (SOD) activity (PubMed:31753489).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Publication Abstract from PubMed

The plant seed proteins referred to as vicilins belong to a structurally common superfamily. While some of them are reported to exhibit superoxide dismutase activity, vicilins from other sources do not possess this activity. Vicilin from Corylus avellana (HZ.1) and Solanum lycopersicum (SL80.1) were purified and subjected to structure-function analysis. The superoxide dismutase activity assays were performed to understand the functional differences between them. While SL80.1 has the superoxide dismutase activity, HZ.1 was enzymatically inactive. Crystal structure followed by mass spectrometry analysis of both the proteins revealed that while SL80.1 has bound salicylic acid, HZ.1 does not. Comparison of C-terminal binding pocket of both the structures revealed that a point mutation at residue 321 in HZ.1 (Gly-->Cys) leads to obstruction in binding of salicylic acid in the pocket. Similarly, copper-binding loop of HZ.1 was reportedly found to be intact and shorter than the loops reported in SL80.1. The copper-binding loop of SL80.1 is rich in polar residues and the absence of these residues in HZ.1 copper-binding loop possibly indicates deficiency in channeling of oxygen radicals to the active center of the enzyme. Difference in the enzymatic activity of vicilin from two evolutionarily distinct sources is due to mutations in its co-factor binding pocket and copper-binding loop.

Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function.,Shikhi M, Jain A, Salunke DM Biochem Biophys Res Commun. 2019 Nov 18. pii: S0006-291X(19)32192-8. doi:, 10.1016/j.bbrc.2019.11.072. PMID:31753489^[13]

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

References

↑ Shikhi M, Jain A, Salunke DM. Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function. Biochem Biophys Res Commun. 2019 Nov 18. pii: S0006-291X(19)32192-8. doi:, 10.1016/j.bbrc.2019.11.072. PMID:31753489 doi:https://dx.doi.org/10.1016/j.bbrc.2019.11.072
↑ Lauer I, Foetisch K, Kolarich D, Ballmer-Weber BK, Conti A, Altmann F, Vieths S, Scheurer S. Hazelnut (Corylus avellana) vicilin Cor a 11: molecular characterization of a glycoprotein and its allergenic activity. Biochem J. 2004 Oct 15;383(Pt 2):327-34. PMID:15233621 doi:10.1042/BJ20041062
↑ Rigby NM, Marsh J, Sancho AI, Wellner K, Akkerdaas J, van Ree R, Knulst A, Fernández-Rivas M, Brettlova V, Schilte PP, Summer C, Pumphrey R, Shewry PR, Mills EN. The purification and characterisation of allergenic hazelnut seed proteins. Mol Nutr Food Res. 2008 Nov;52 Suppl 2:S251-61. PMID:19006093 doi:10.1002/mnfr.200800083
↑ Iwan M, Vissers YM, Fiedorowicz E, Kostyra H, Kostyra E, Savelkoul HF, Wichers HJ. Impact of Maillard reaction on immunoreactivity and allergenicity of the hazelnut allergen Cor a 11. J Agric Food Chem. 2011 Jul 13;59(13):7163-71. PMID:21563837 doi:10.1021/jf2007375
↑ Ansari P, Stoppacher N, Baumgartner S. Marker peptide selection for the determination of hazelnut by LC-MS/MS and occurrence in other nuts. Anal Bioanal Chem. 2012 Mar;402(8):2607-15. PMID:21735061 doi:10.1007/s00216-011-5218-6
↑ López E, Cuadrado C, Burbano C, Jiménez MA, Rodríguez J, Crespo JF. Effects of autoclaving and high pressure on allergenicity of hazelnut proteins. J Clin Bioinforma. 2012 May 22;2(1):12. PMID:22616776 doi:10.1186/2043-9113-2-12
↑ Verweij MM, Hagendorens MM, Trashin S, Cucu T, De Meulenaer B, Devreese B, Bridts CH, De Clerck LS, Ebo DG. Age-dependent sensitization to the 7S-vicilin-like protein Cor a 11 from hazelnut (Corylus avellana) in a birch-endemic region. J Investig Allergol Clin Immunol. 2012;22(4):245-51 PMID:22812192
↑ Cucu T, De Meulenaer B, Devreese B. MALDI-based identification of stable hazelnut protein derived tryptic marker peptides. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2012;29(12):1821-31. PMID:22966848 doi:10.1080/19440049.2012.719639
↑ Iniesto E, Jiménez A, Prieto N, Cabanillas B, Burbano C, Pedrosa MM, Rodríguez J, Muzquiz M, Crespo JF, Cuadrado C, Linacero R. Real Time PCR to detect hazelnut allergen coding sequences in processed foods. Food Chem. 2013 Jun 1;138(2-3):1976-81. PMID:23411333 doi:10.1016/j.foodchem.2012.11.036
↑ Costa J, Ansari P, Mafra I, Oliveira MB, Baumgartner S. Assessing hazelnut allergens by protein ELISA and real-time PCR. Anal Bioanal Chem. 2014 Apr;406(11):2581-90. PMID:24577577 doi:10.1007/s00216-014-7679-x
↑ De Ceglie C, Calvano CD, Zambonin CG. Determination of hidden hazelnut oil proteins in extra virgin olive oil by cold acetone precipitation followed by in-solution tryptic digestion and MALDI-TOF-MS analysis. J Agric Food Chem. 2014 Oct 1;62(39):9401-9. PMID:25209075 doi:10.1021/jf504007d
↑ Costa J, Ansari P, Mafra I, Oliveira MB, Baumgartner S. Assessing hazelnut allergens by protein ELISA and real-time PCR. Anal Bioanal Chem. 2014 Apr;406(11):2581-90. PMID:24577577 doi:10.1007/s00216-014-7679-x
↑ Shikhi M, Jain A, Salunke DM. Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function. Biochem Biophys Res Commun. 2019 Nov 18. pii: S0006-291X(19)32192-8. doi:, 10.1016/j.bbrc.2019.11.072. PMID:31753489 doi:https://dx.doi.org/10.1016/j.bbrc.2019.11.072

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Shikhi M, Jain A, Salunke DM. Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function. Biochem Biophys Res Commun. 2019 Nov 18. pii: S0006-291X(19)32192-8. doi:, 10.1016/j.bbrc.2019.11.072. PMID:31753489 doi:https://dx.doi.org/10.1016/j.bbrc.2019.11.072

[2] Lauer I, Foetisch K, Kolarich D, Ballmer-Weber BK, Conti A, Altmann F, Vieths S, Scheurer S. Hazelnut (Corylus avellana) vicilin Cor a 11: molecular characterization of a glycoprotein and its allergenic activity. Biochem J. 2004 Oct 15;383(Pt 2):327-34. PMID:15233621 doi:10.1042/BJ20041062

[3] Rigby NM, Marsh J, Sancho AI, Wellner K, Akkerdaas J, van Ree R, Knulst A, Fernández-Rivas M, Brettlova V, Schilte PP, Summer C, Pumphrey R, Shewry PR, Mills EN. The purification and characterisation of allergenic hazelnut seed proteins. Mol Nutr Food Res. 2008 Nov;52 Suppl 2:S251-61. PMID:19006093 doi:10.1002/mnfr.200800083

[4] Iwan M, Vissers YM, Fiedorowicz E, Kostyra H, Kostyra E, Savelkoul HF, Wichers HJ. Impact of Maillard reaction on immunoreactivity and allergenicity of the hazelnut allergen Cor a 11. J Agric Food Chem. 2011 Jul 13;59(13):7163-71. PMID:21563837 doi:10.1021/jf2007375

[5] Ansari P, Stoppacher N, Baumgartner S. Marker peptide selection for the determination of hazelnut by LC-MS/MS and occurrence in other nuts. Anal Bioanal Chem. 2012 Mar;402(8):2607-15. PMID:21735061 doi:10.1007/s00216-011-5218-6

[6] López E, Cuadrado C, Burbano C, Jiménez MA, Rodríguez J, Crespo JF. Effects of autoclaving and high pressure on allergenicity of hazelnut proteins. J Clin Bioinforma. 2012 May 22;2(1):12. PMID:22616776 doi:10.1186/2043-9113-2-12

[7] Verweij MM, Hagendorens MM, Trashin S, Cucu T, De Meulenaer B, Devreese B, Bridts CH, De Clerck LS, Ebo DG. Age-dependent sensitization to the 7S-vicilin-like protein Cor a 11 from hazelnut (Corylus avellana) in a birch-endemic region. J Investig Allergol Clin Immunol. 2012;22(4):245-51 PMID:22812192

[8] Cucu T, De Meulenaer B, Devreese B. MALDI-based identification of stable hazelnut protein derived tryptic marker peptides. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2012;29(12):1821-31. PMID:22966848 doi:10.1080/19440049.2012.719639

[9] Iniesto E, Jiménez A, Prieto N, Cabanillas B, Burbano C, Pedrosa MM, Rodríguez J, Muzquiz M, Crespo JF, Cuadrado C, Linacero R. Real Time PCR to detect hazelnut allergen coding sequences in processed foods. Food Chem. 2013 Jun 1;138(2-3):1976-81. PMID:23411333 doi:10.1016/j.foodchem.2012.11.036

[10] Costa J, Ansari P, Mafra I, Oliveira MB, Baumgartner S. Assessing hazelnut allergens by protein ELISA and real-time PCR. Anal Bioanal Chem. 2014 Apr;406(11):2581-90. PMID:24577577 doi:10.1007/s00216-014-7679-x

[11] De Ceglie C, Calvano CD, Zambonin CG. Determination of hidden hazelnut oil proteins in extra virgin olive oil by cold acetone precipitation followed by in-solution tryptic digestion and MALDI-TOF-MS analysis. J Agric Food Chem. 2014 Oct 1;62(39):9401-9. PMID:25209075 doi:10.1021/jf504007d

[12] Costa J, Ansari P, Mafra I, Oliveira MB, Baumgartner S. Assessing hazelnut allergens by protein ELISA and real-time PCR. Anal Bioanal Chem. 2014 Apr;406(11):2581-90. PMID:24577577 doi:10.1007/s00216-014-7679-x

[13] Shikhi M, Jain A, Salunke DM. Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function. Biochem Biophys Res Commun. 2019 Nov 18. pii: S0006-291X(19)32192-8. doi:, 10.1016/j.bbrc.2019.11.072. PMID:31753489 doi:https://dx.doi.org/10.1016/j.bbrc.2019.11.072

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@@ Line 3: / Line 3: @@
 <StructureSection load='6l4c' size='340' side='right'caption='[[6l4c]], [[Resolution|resolution]] 3.19&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6l4c]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Corylus_avellana Corylus avellana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L4C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L4C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6l4c]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Corylus_avellana Corylus avellana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L4C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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]] 3.191&#8491;</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=6l4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l4c OCA], [http://pdbe.org/6l4c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l4c RCSB], [http://www.ebi.ac.uk/pdbsum/6l4c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l4c ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></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=6l4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l4c OCA], [https://pdbe.org/6l4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l4c RCSB], [https://www.ebi.ac.uk/pdbsum/6l4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l4c ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/VCL_CORAV VCL_CORAV] Seed storage protein (PubMed:15233621, PubMed:19006093, PubMed:21563837, PubMed:21735061, PubMed:22966848, PubMed:22616776, PubMed:22812192, PubMed:23411333, Ref.12, PubMed:24577577, PubMed:25209075). Does not have superoxide dismutase (SOD) activity (PubMed:31753489).<ref>PMID:31753489</ref> <ref>PMID:15233621</ref> <ref>PMID:19006093</ref> <ref>PMID:21563837</ref> <ref>PMID:21735061</ref> <ref>PMID:22616776</ref> <ref>PMID:22812192</ref> <ref>PMID:22966848</ref> <ref>PMID:23411333</ref> <ref>PMID:24577577</ref> <ref>PMID:25209075</ref> <ref>PMID:24577577</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 25: @@
 [[Category: Corylus avellana]]
 [[Category: Large Structures]]
-[[Category: Salunke, D M]]
+[[Category: Salunke DM]]
-[[Category: Shikhi, M]]
+[[Category: Shikhi M]]
-[[Category: Copper binding protein]]
-[[Category: Electrostatic loop]]
-[[Category: Plant protein]]
-[[Category: Plant seed protein]]
-[[Category: Superoxide dismutase activity]]

6l4c: Difference between revisions

Latest revision as of 10:51, 22 November 2023

Crystal structure of vicilin from Corylus avellana (Hazelnut)

Structural highlights

Function

Publication Abstract from PubMed

References

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