5kxc: Difference between revisions

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-'''Unreleased structure'''
-The entry 5kxc is ON HOLD
+==Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 8.5.==
+<StructureSection load='5kxc' size='340' side='right'caption='[[5kxc]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5kxc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KXC 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6Y2:~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-ACETAMIDO-2-(HYDROXYMETHYL)-6-(4-NITROPHENOXY)-4-OXIDANYL-OXAN-3-YL]OXY-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-3-YL]ETHANAMIDE'>6Y2</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5kxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxc OCA], [https://pdbe.org/5kxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kxc RCSB], [https://www.ebi.ac.uk/pdbsum/5kxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A1D5B395_WISFL A0A1D5B395_WISFL]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aberrant glycosylation and the overexpression of specific carbohydrate epitopes is a hallmark of many cancers, and tumor-associated oligo-saccharides are actively investigated as targets for immunotherapy and diagnostics. Wisteria floribunda agglutinin (WFA) is a legume lectin that recognizes terminal N-acetylgalactosaminides with high affinity. WFA preferentially binds the disaccharide LacdiNAc (beta-D-GalNAc-[1--&gt;4]-D-GlcNAc), which is associated with tumor malignancy in leukemia, prostate, pancreatic, ovarian, and liver cancers, and has shown promise in cancer glycobiomarker detection. The mechanism of specificity for WFA recognition of LacdiNAc is not fully understood. To address this problem, we have determined affinities and structure of WFA in complex with GalNAc and LacdiNAc. Affinities towards Gal, GalNAc, and LacdiNAc were measured via surface plasmon resonance, yielding KD values of 4.67 x 10-4 M, 9.24 x 10-5 M, and 5.45 x 10-6 M respectively. Structures of WFA in complex with LacdiNAc and GalNAc have been determined to 1.80 A - 2.32 A resolution. These high-resolution structures revealed a hydrophobic groove complementary to the GalNAc and, to a minor extent, to the backface of the GlcNAc sugar ring. Remarkably, the contribution of this small hydrophobic surface significantly increases the observed affinity for LacdiNAc over GalNAc. Tandem MS sequencing confirmed presence of two isolectin forms in commercially available WFA differing only in the identities of two amino acids. Finally, the WFA carbohydrate binding site is similar to a homologous lectin isolated from Vatairea macrocarpa in complex with GalNAc which, unlike WFA, binds not only alphaGalNAc but also terminal Ser/Thr O-linked alphaGalNAc (Tn antigen).
-Authors: Evans, S.V., Haji-Ghassemi, O.
+Molecular basis for recognition of the cancer glycobiomarker LacdiNAc (GalNAc(beta1-4)GlcNAc) by Wisteria floribunda agglutinin.,Haji-Ghassemi O, Gilbert M, Spence J, Schur MJ, Parker MJ, Jenkins ML, Burke JE, van Faassen H, Young NM, Evans SV J Biol Chem. 2016 Sep 6. pii: jbc.M116.750463. PMID:27601469<ref>PMID:27601469</ref>
-Description: Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 8.5.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Evans, S.V]]
+<div class="pdbe-citations 5kxc" style="background-color:#fffaf0;"></div>
-[[Category: Haji-Ghassemi, O]]
+==See Also==
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Wisteria floribunda]]
+[[Category: Evans SV]]
+[[Category: Haji-Ghassemi O]]