2gdf: Difference between revisions

Latest revision as of 13:51, 13 March 2024

Crystal structure of Dioclea violacea seed lectin

Structural highlights

2gdf is a 4 chain structure with sequence from Macropsychanthus violaceus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	CA, MN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LECA_DIOGR D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 50 ug/ml.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Barral-Netto M, Santos SB, Barral A, Moreira LI, Santos CF, Moreira RA, Oliveira JT, Cavada BS. Human lymphocyte stimulation by legume lectins from the Diocleae tribe. Immunol Invest. 1992 Jul;21(4):297-303. PMID:1398779
↑ Gomes JC, Ferreira RR, Cavada BS, Moreira RA, Oliveira JT. Histamine release induced by glucose (mannose)-specific lectins isolated from Brazilian beans. Comparison with concanavalin A. Agents Actions. 1994 May;41(3-4):132-5. PMID:7524287
↑ Assreuy AM, Shibuya MD, Martins GJ, De Souza ML, Cavada BS, Moreira RA, Oliveira JT, Ribeiro RA, Flores CA. Anti-inflammatory effect of glucose-mannose binding lectins isolated from Brazilian beans. Mediators Inflamm. 1997;6(3):201-10. PMID:18472821 doi:https://dx.doi.org/10.1080/09629359791695
↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, de Sousa FA, Oscarson S, Brewer CF. Diocleinae lectins are a group of proteins with conserved binding sites for the core trimannoside of asparagine-linked oligosaccharides and differential specificities for complex carbohydrates. J Biol Chem. 1998 May 15;273(20):12082-8. PMID:9575151
↑ Dam TK, Cavada BS, Grangeiro TB, Santos CF, Ceccatto VM, de Sousa FA, Oscarson S, Brewer CF. Thermodynamic binding studies of lectins from the diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides. J Biol Chem. 2000 May 26;275(21):16119-26. PMID:10747944 doi:https://dx.doi.org/10.1074/jbc.M000670200
↑ dos Santos AF, Cavada BS, da Rocha BA, do Nascimento KS, Sant'Ana AE. Toxicity of some glucose/mannose-binding lectins to Biomphalaria glabrata and Artemia salina. Bioresour Technol. 2010 Jan;101(2):794-8. doi: 10.1016/j.biortech.2009.07.062., Epub 2009 Sep 17. PMID:19765980 doi:https://dx.doi.org/10.1016/j.biortech.2009.07.062

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OCA

[1] Barral-Netto M, Santos SB, Barral A, Moreira LI, Santos CF, Moreira RA, Oliveira JT, Cavada BS. Human lymphocyte stimulation by legume lectins from the Diocleae tribe. Immunol Invest. 1992 Jul;21(4):297-303. PMID:1398779

[2] Gomes JC, Ferreira RR, Cavada BS, Moreira RA, Oliveira JT. Histamine release induced by glucose (mannose)-specific lectins isolated from Brazilian beans. Comparison with concanavalin A. Agents Actions. 1994 May;41(3-4):132-5. PMID:7524287

[3] Assreuy AM, Shibuya MD, Martins GJ, De Souza ML, Cavada BS, Moreira RA, Oliveira JT, Ribeiro RA, Flores CA. Anti-inflammatory effect of glucose-mannose binding lectins isolated from Brazilian beans. Mediators Inflamm. 1997;6(3):201-10. PMID:18472821 doi:https://dx.doi.org/10.1080/09629359791695

[4] Dam TK, Cavada BS, Grangeiro TB, Santos CF, de Sousa FA, Oscarson S, Brewer CF. Diocleinae lectins are a group of proteins with conserved binding sites for the core trimannoside of asparagine-linked oligosaccharides and differential specificities for complex carbohydrates. J Biol Chem. 1998 May 15;273(20):12082-8. PMID:9575151

[5] Dam TK, Cavada BS, Grangeiro TB, Santos CF, Ceccatto VM, de Sousa FA, Oscarson S, Brewer CF. Thermodynamic binding studies of lectins from the diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides. J Biol Chem. 2000 May 26;275(21):16119-26. PMID:10747944 doi:https://dx.doi.org/10.1074/jbc.M000670200

[6] s Santos AF, Cavada BS, da Rocha BA, do Nascimento KS, Sant'Ana AE. Toxicity of some glucose/mannose-binding lectins to Biomphalaria glabrata and Artemia salina. Bioresour Technol. 2010 Jan;101(2):794-8. doi: 10.1016/j.biortech.2009.07.062., Epub 2009 Sep 17. PMID:19765980 doi:https://dx.doi.org/10.1016/j.biortech.2009.07.062

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@@ Line 1: / Line 1: @@
-[[Image:2gdf.png|left|200px]]
-{{STRUCTURE_2gdf|  PDB=2gdf  |  SCENE=  }}
+==Crystal structure of Dioclea violacea seed lectin==
+<StructureSection load='2gdf' size='340' side='right'caption='[[2gdf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-===Crystal structure of Dioclea violacea seed lectin===
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2gdf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macropsychanthus_violaceus Macropsychanthus violaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GDF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-==About this Structure==
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-[[2gdf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_violacea Dioclea violacea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDF OCA].
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gdf OCA], [https://pdbe.org/2gdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gdf RCSB], [https://www.ebi.ac.uk/pdbsum/2gdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gdf ProSAT]</span></td></tr>
-[[Category: Dioclea violacea]]
+</table>
-[[Category: Cavada, B S.]]
+== Function ==
-[[Category: Chornet, J J.C.]]
+[https://www.uniprot.org/uniprot/LECA_DIOGR LECA_DIOGR] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 50 ug/ml.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</ref>
-[[Category: Sol, F Gallego del.]]
+== Evolutionary Conservation ==
-[[Category: Plant lectin]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Sugar binding protein]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/2gdf_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/main_output.php?pdb_ID=2gdf ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Macropsychanthus violaceus]]
+[[Category: Cavada BS]]
+[[Category: Chornet JJC]]
+[[Category: Gallego del Sol F]]

2gdf: Difference between revisions

Latest revision as of 13:51, 13 March 2024

Crystal structure of Dioclea violacea seed lectin

Structural highlights

Function

Evolutionary Conservation

References

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