5av7

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Calsepa lectin in complex with bisected glycan

Structural highlights

5av7 is a 4 chain structure with sequence from Calystegia sepium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LECC_CALSE Mannose-binding lectin (PubMed:9111143, PubMed:18266762, PubMed:14561768, PubMed:26971576, PubMed:28973127). Preferentially binds mannose at concentrations ranging between 5 and 25 mM, but binds also glucose. Has a marked preference for methylated sugar derivatives, such as alpha-MeMan and alpha-MeGlc, at concentration down to 5 mM (PubMed:14561768). Binds to N-glycans, but not to glycolipid-type or other type of glycans (PubMed:28973127). Binds N-linked high-mannose-type glycans (PubMed:18266762, PubMed:28973127). Has a preference for smaller (Man(2)-Man(6)) high-mannose-type glycans to larger (Man(7)-Man(9)) ones. Recognizes both alpha1-6 extended and alpha1-3 extended monoantennary glycans. The addition of alpha1-2Man to the Man-alpha1-3Man-beta branch results in a significant loss of affinity, but beta1-2GlcNAc has some affinity. Has less affinity for biantennary glycans (PubMed:18266762). However, affinity is significant for the biantennary complex-type N-glycans with bisecting GlcNAc (PubMed:18266762, PubMed:26971576, PubMed:28973127). No affinity is observed for tri- and tetra-antennary glycans (PubMed:18266762). Binds bisected glycans of the mouse brain. Selectively binds to bisecting N-glycans which are in back-fold conformation, and does not favor a glycan with an extend conformation (PubMed:26971576). Has hemagglutinating activity against rabbit erythrocytes at 0.3 ug/ml and against trypsin-treated human erythrocytes at 5 ug/ml. Has mitogenic activity in murine cells (PubMed:9111143).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Glycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylglucosamine (GlcNAc), is potentially a good model for investigating conformational dynamics and glycan-lectin interactions, owing to the unique ability of this sugar residue to alter conformer populations and thus modulate the biological activities. Here we analyzed bisected glycan in complex with two unrelated lectins, Calsepa and PHA-E. The crystal structures of the two complexes show a conspicuous flipped back glycan structure (designated 'back-fold' conformation), and solution NMR analysis also provides evidence of 'back-fold' glycan structure. Indeed, statistical conformational analysis of available bisected and non-bisected glycan structures suggests that bisecting GlcNAc restricts the conformations of branched structures. Restriction of glycan flexibility by certain sugar residues may be more common than previously thought and impinges on the mechanism of glycoform-dependent biological functions.

Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins.,Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y Sci Rep. 2016 Mar 14;6:22973. doi: 10.1038/srep22973. PMID:26971576^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bourne Y, Roig-Zamboni V, Barre A, Peumans WJ, Astoul CH, Van Damme EJ, Rouge P. The crystal structure of the Calystegia sepium agglutinin reveals a novel quaternary arrangement of lectin subunits with a beta-prism fold. J Biol Chem. 2004 Jan 2;279(1):527-33. Epub 2003 Oct 15. PMID:14561768 doi:10.1074/jbc.M308218200
↑ Nakamura-Tsuruta S, Uchiyama N, Peumans WJ, Van Damme EJ, Totani K, Ito Y, Hirabayashi J. Analysis of the sugar-binding specificity of mannose-binding-type Jacalin-related lectins by frontal affinity chromatography--an approach to functional classification. FEBS J. 2008 Mar;275(6):1227-39. PMID:18266762 doi:10.1111/j.1742-4658.2008.06282.x
↑ Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y. Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins. Sci Rep. 2016 Mar 14;6:22973. doi: 10.1038/srep22973. PMID:26971576 doi:http://dx.doi.org/10.1038/srep22973
↑ Nagae M, Mishra SK, Hanashima S, Tateno H, Yamaguchi Y. Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa. Glycobiology. 2017 Sep 7. doi: 10.1093/glycob/cwx081. PMID:28973127 doi:http://dx.doi.org/10.1093/glycob/cwx081
↑ Peumans WJ, Winter HC, Bemer V, Van Leuven F, Goldstein IJ, Truffa-Bachi P, Van Damme EJ. Isolation of a novel plant lectin with an unusual specificity from Calystegia sepium. Glycoconj J. 1997 Feb;14(2):259-65. PMID:9111143 doi:10.1023/a:1018502107707
↑ Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y. Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins. Sci Rep. 2016 Mar 14;6:22973. doi: 10.1038/srep22973. PMID:26971576 doi:http://dx.doi.org/10.1038/srep22973

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5av7"

Categories: Calystegia sepium | Large Structures | Nagae M | Yamaguchi Y

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[5av7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Calystegia_sepium Calystegia sepium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AV7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</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=5av7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5av7 OCA], [https://pdbe.org/5av7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5av7 RCSB], [https://www.ebi.ac.uk/pdbsum/5av7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5av7 ProSAT]</span></td></tr>
 </table>

5av7

From Proteopedia

Current revision

Crystal structure of Calsepa lectin in complex with bisected glycan

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox