2e7q: Difference between revisions
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< | ==Crystal structure of basic winged bean lectin in complex with b blood group trisaccharide== | ||
<StructureSection load='2e7q' size='340' side='right'caption='[[2e7q]], [[Resolution|resolution]] 2.75Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2e7q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Psophocarpus_tetragonolobus Psophocarpus tetragonolobus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E7Q 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]] 2.75Å</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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=2e7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e7q OCA], [https://pdbe.org/2e7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e7q RCSB], [https://www.ebi.ac.uk/pdbsum/2e7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e7q ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/LEC1_PSOTE LEC1_PSOTE] Lectin. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/2e7q_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2e7q ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Basic winged bean agglutinin binds A-blood group substance with higher affinity and B-blood group substance with lesser affinity. It does not bind the O substance. The crystal structures of the lectin, complexed with A-reactive and B-reactive di and tri saccharides, have been determined. In addition, the complexes of the lectin with fucosylated A-trisaccharides and B-trisaccharides and with a variant of the A-trisaccharide have been modeled. These structures and models provide valuable insights into the structural basis of blood group specificities. All the four carbohydrate binding loops of the lectin contribute to the primary combining site while the loop of variable length contributes to the secondary binding site. In a significant advance to the current understanding, the interactions at the secondary binding site also contribute substantially, albeit in a subtle manner, to determine the blood group specificity. Compared with the interactions of the B-trisaccharide with the lectin, the third sugar residue of the A-reactive trisacharide forms an additional hydrogen bond with a lysine residue in the variable loop. In the former, the formation of such a hydrogen bond is prevented by a shift in the orientation of third sugar resulting from an internal hydrogen bond in it. The formation of this bond is also facilitated by an interaction dependent change in the rotamer conformation of the lysyl residue of the variable loop. Thus, the difference in the interactions at the secondary site is generated by coordinated movements in the ligand as well as the protein. A comparison of the crystal structure and the model of the complex involving the variant of the A-trisaccharide results in the delineation of the relative contributions of the interactions at the primary and the secondary sites in determining blood group specificity. | |||
Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin.,Kulkarni KA, Katiyar S, Surolia A, Vijayan M, Suguna K Proteins. 2007 Aug 15;68(3):762-9. PMID:17510954<ref>PMID:17510954</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2e7q" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Agglutinin 3D structures|Agglutinin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: Psophocarpus tetragonolobus]] | [[Category: Psophocarpus tetragonolobus]] | ||
[[Category: Katiyar S]] | |||
[[Category: Katiyar | [[Category: Kulkarni KA]] | ||
[[Category: Kulkarni | [[Category: Suguna K]] | ||
[[Category: Suguna | [[Category: Surolia A]] | ||
[[Category: Surolia | [[Category: Vijayan M]] | ||
[[Category: Vijayan | |||
Latest revision as of 10:52, 23 October 2024
Crystal structure of basic winged bean lectin in complex with b blood group trisaccharideCrystal structure of basic winged bean lectin in complex with b blood group trisaccharide
Structural highlights
FunctionLEC1_PSOTE Lectin. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedBasic winged bean agglutinin binds A-blood group substance with higher affinity and B-blood group substance with lesser affinity. It does not bind the O substance. The crystal structures of the lectin, complexed with A-reactive and B-reactive di and tri saccharides, have been determined. In addition, the complexes of the lectin with fucosylated A-trisaccharides and B-trisaccharides and with a variant of the A-trisaccharide have been modeled. These structures and models provide valuable insights into the structural basis of blood group specificities. All the four carbohydrate binding loops of the lectin contribute to the primary combining site while the loop of variable length contributes to the secondary binding site. In a significant advance to the current understanding, the interactions at the secondary binding site also contribute substantially, albeit in a subtle manner, to determine the blood group specificity. Compared with the interactions of the B-trisaccharide with the lectin, the third sugar residue of the A-reactive trisacharide forms an additional hydrogen bond with a lysine residue in the variable loop. In the former, the formation of such a hydrogen bond is prevented by a shift in the orientation of third sugar resulting from an internal hydrogen bond in it. The formation of this bond is also facilitated by an interaction dependent change in the rotamer conformation of the lysyl residue of the variable loop. Thus, the difference in the interactions at the secondary site is generated by coordinated movements in the ligand as well as the protein. A comparison of the crystal structure and the model of the complex involving the variant of the A-trisaccharide results in the delineation of the relative contributions of the interactions at the primary and the secondary sites in determining blood group specificity. Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin.,Kulkarni KA, Katiyar S, Surolia A, Vijayan M, Suguna K Proteins. 2007 Aug 15;68(3):762-9. PMID:17510954[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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