3rs6: Difference between revisions

Latest revision as of 09:44, 1 March 2024

Crystal structure Dioclea virgata lectin in complexed with X-mannose

Structural highlights

3rs6 is a 1 chain structure with sequence from Dioclea virgata. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	CA, MN, XMM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LECA_DIOVI D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 20 ug/ml.[REFERENCE:1]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

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
↑ Ferreira RR, Cavada BS, Moreira RA, Oliveira JT, Gomes JC. Characteristics of the histamine release from hamster cheek pouch mast cells stimulated by lectins from Brazilian beans and concanavalin A. Inflamm Res. 1996 Sep;45(9):442-7. PMID:8891754
↑ 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] Ferreira RR, Cavada BS, Moreira RA, Oliveira JT, Gomes JC. Characteristics of the histamine release from hamster cheek pouch mast cells stimulated by lectins from Brazilian beans and concanavalin A. Inflamm Res. 1996 Sep;45(9):442-7. PMID:8891754

[4] 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

[5] 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

[6] 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

[7] 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

[1]

[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3rs6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dioclea_virgata Dioclea virgata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RS6 FirstGlance]. <br>
-</td></tr><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>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rrd|3rrd]]</div></td></tr>
+<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>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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=3rs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rs6 OCA], [https://pdbe.org/3rs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rs6 RCSB], [https://www.ebi.ac.uk/pdbsum/3rs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rs6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/LECA_DIOVI LECA_DIOVI]] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 20 ug/ml.[REFERENCE:1]<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:8891754</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</ref>
+[https://www.uniprot.org/uniprot/LECA_DIOVI LECA_DIOVI] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 20 ug/ml.[REFERENCE:1]<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:8891754</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The lectin of Dioclea virgata (DvirL), both native and complexed with X-man, was submitted to X-ray diffraction analysis and the crystal structure was compared to that of other Diocleinae lectins in order to better understand differences in biological properties, especially with regard to the ability of lectins to induce nitric oxide (NO) production. An association was observed between the volume of the carbohydrate recognition domain (CRD), the ability to induce NO production and the relative positions of Tyr12, Arg228 and Leu99. Thus, differences in biological activity induced by Diocleinae lectins are related to the configuration of amino acid residues in the carbohydrate binding site and to the structural conformation of subsequent regions capable of influencing site-ligand interactions. In conclusion, the ability of Diocleinae lectins to induce NO production depends on CRD configuration.
-Structure of Dioclea virgata lectin: Relations between carbohydrate binding site and nitric oxide production.,Batista da Nobrega R, Rocha BA, Gadelha CA, Santi-Gadelha T, Pires AF, Assreuy AM, Nascimento KS, Nagano CS, Sampaio AH, Cavada BS, Delatorre P Biochimie. 2011 Dec 16. PMID:22198239<ref>PMID:22198239</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3rs6" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 25: / Line 16: @@
 [[Category: Dioclea virgata]]
 [[Category: Large Structures]]
-[[Category: Alencar, K L]]
+[[Category: Alencar KL]]
-[[Category: Bezerra, E H.S]]
+[[Category: Bezerra EHS]]
-[[Category: Bezerra, M J.B]]
+[[Category: Bezerra MJB]]
-[[Category: Gadelha, C A.A]]
+[[Category: Gadelha CAA]]
-[[Category: Nagano, C S]]
+[[Category: Nagano CS]]
-[[Category: Santi-Gadelha, T]]
+[[Category: Santi-Gadelha T]]
-[[Category: Silva-Filho, J C]]
+[[Category: Silva-Filho JC]]
-[[Category: Carboydrate binding protein]]
-[[Category: Lectin]]
-[[Category: Leguminose]]
-[[Category: Seed dioclea virgata]]
-[[Category: Sugar binding protein]]
-[[Category: X-mannose]]

3rs6: Difference between revisions

Latest revision as of 09:44, 1 March 2024

Crystal structure Dioclea virgata lectin in complexed with X-mannose

Structural highlights

Function

References

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