6vgf: Difference between revisions
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==Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD)== | ==Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD)== | ||
<StructureSection load='6vgf' size='340' side='right'caption='[[6vgf]]' scene=''> | <StructureSection load='6vgf' size='340' side='right'caption='[[6vgf]], [[Resolution|resolution]] 1.83Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VGF OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6vgf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arachis_hypogaea Arachis hypogaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VGF FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83Å</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=WA3:(2S,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({4-[({[(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-2-yl]methyl}sulfanyl)methyl]-1H-1,2,3-triazol-1-yl}methyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol'>WA3</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=6vgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vgf OCA], [https://pdbe.org/6vgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vgf RCSB], [https://www.ebi.ac.uk/pdbsum/6vgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vgf ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/LECG_ARAHY LECG_ARAHY] D-galactose specific lectin. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Carbohydrate-lectin interactions are involved in important cellular recognition processes, including viral and bacterial infections, inflammation and tumor metastasis. Hence, structural studies of lectin-synthetic glycan complexes are essential for understanding lectin-recognition processes and for the further design of promising chemotherapeutics that interfere with sugar-lectin interactions. Plant lectins are excellent models for the study of the molecular-recognition process. Among them, peanut lectin (PNA) is highly relevant in the field of glycobiology because of its specificity for beta-galactosides, showing high affinity towards the Thomsen-Friedenreich antigen, a well known tumor-associated carbohydrate antigen. Given this specificity, PNA is one of the most frequently used molecular probes for the recognition of tumor cell-surface O-glycans. Thus, it has been extensively used in glycobiology for inhibition studies with a variety of beta-galactoside and beta-lactoside ligands. Here, crystal structures of PNA are reported in complex with six novel synthetic hydrolytically stable beta-N- and beta-S-galactosides. These complexes disclosed key molecular-binding interactions of the different sugars with PNA at the atomic level, revealing the roles of specific water molecules in protein-ligand recognition. Furthermore, binding-affinity studies by isothermal titration calorimetry showed dissociation-constant values in the micromolar range, as well as a positive multivalency effect in terms of affinity in the case of the divalent compounds. Taken together, this work provides a qualitative structural rationale for the upcoming synthesis of optimized glycoclusters designed for the study of lectin-mediated biological processes. The understanding of the recognition of beta-N- and beta-S-galactosides by PNA represents a benchmark in protein-carbohydrate interactions since they are novel synthetic ligands that do not belong to the family of O-linked glycosides. | |||
Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands.,Cagnoni AJ, Primo ED, Klinke S, Cano ME, Giordano W, Marino KV, Kovensky J, Goldbaum FA, Uhrig ML, Otero LH Acta Crystallogr D Struct Biol. 2020 Nov 1;76(Pt 11):1080-1091. doi:, 10.1107/S2059798320012371. Epub 2020 Oct 13. PMID:33135679<ref>PMID:33135679</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6vgf" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Galactose-binding lectin|Galactose-binding lectin]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Arachis hypogaea]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Cagnoni AJ]] | [[Category: Cagnoni AJ]] | ||
Latest revision as of 11:12, 11 October 2023
Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD)Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD)
Structural highlights
FunctionLECG_ARAHY D-galactose specific lectin. Publication Abstract from PubMedCarbohydrate-lectin interactions are involved in important cellular recognition processes, including viral and bacterial infections, inflammation and tumor metastasis. Hence, structural studies of lectin-synthetic glycan complexes are essential for understanding lectin-recognition processes and for the further design of promising chemotherapeutics that interfere with sugar-lectin interactions. Plant lectins are excellent models for the study of the molecular-recognition process. Among them, peanut lectin (PNA) is highly relevant in the field of glycobiology because of its specificity for beta-galactosides, showing high affinity towards the Thomsen-Friedenreich antigen, a well known tumor-associated carbohydrate antigen. Given this specificity, PNA is one of the most frequently used molecular probes for the recognition of tumor cell-surface O-glycans. Thus, it has been extensively used in glycobiology for inhibition studies with a variety of beta-galactoside and beta-lactoside ligands. Here, crystal structures of PNA are reported in complex with six novel synthetic hydrolytically stable beta-N- and beta-S-galactosides. These complexes disclosed key molecular-binding interactions of the different sugars with PNA at the atomic level, revealing the roles of specific water molecules in protein-ligand recognition. Furthermore, binding-affinity studies by isothermal titration calorimetry showed dissociation-constant values in the micromolar range, as well as a positive multivalency effect in terms of affinity in the case of the divalent compounds. Taken together, this work provides a qualitative structural rationale for the upcoming synthesis of optimized glycoclusters designed for the study of lectin-mediated biological processes. The understanding of the recognition of beta-N- and beta-S-galactosides by PNA represents a benchmark in protein-carbohydrate interactions since they are novel synthetic ligands that do not belong to the family of O-linked glycosides. Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands.,Cagnoni AJ, Primo ED, Klinke S, Cano ME, Giordano W, Marino KV, Kovensky J, Goldbaum FA, Uhrig ML, Otero LH Acta Crystallogr D Struct Biol. 2020 Nov 1;76(Pt 11):1080-1091. doi:, 10.1107/S2059798320012371. Epub 2020 Oct 13. PMID:33135679[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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