This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5xfi

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of Calsepa lectin in complex with biantennary N-glycan

Structural highlights

5xfi is a 2 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 1.653Å
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

Mannose-binding type Jacalin-related lectins (mJRLs) bind to branched N-glycans via conserved sugar binding sites. Despite significant 3D structural similarities, each mJRL is known to have a unique binding preference towards various N-glycans. However, the molecular basis of varying binding preference is substantially unknown. Here we report a detailed comparison of N-glycan binding preference for two mJRLs, Orysata and Calsepa using frontal affinity chromatography (FAC), X-ray and molecular modeling. The FAC analysis using a panel of N-glycans shows difference in N-glycan binding preference between the lectins. Orysata shows broader specificity toward most high-mannose-type glycans as well as biantennary complex-type glycans bearing an extension on the Manalpha1-6 branch. Whereas, Calsepa shows narrow specificity to complex-type glycans with bisecting GlcNAc. The X-ray crystallographic structure reveals that two Orysata lectins bind to one biantennary N-glycan (2:1 binding) where one lectin binds to mannose of the alpha1-3 branch, while the other interacts with an N-acetylglucosamine of the alpha1-6 branch. In contrast, Calsepa shows 1:1 binding where alpha1-3 branch and core chitobiose region N-glycan interacts with lectin, while alpha1-6 branch is flipped back to the chitobiose core. Molecular dynamics study of Orysata bound to N-glycans substantiate possibility of two binding modes for each N-glycan. Binding free energies calculated separately for alpha1-3 and alpha1-6 branches of each N-glycan suggest both branches can bind to Orysata. Overall these results suggest that each branch of N-glycan has a distinct role in binding mJRLs and the non-binding branch can contribute significantly to the binding affinity and hence to the specificity.

Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa.,Nagae M, Mishra SK, Hanashima S, Tateno H, Yamaguchi Y Glycobiology. 2017 Sep 7. doi: 10.1093/glycob/cwx081. PMID:28973127^[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, 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

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/5xfi"

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of Calsepa lectin in complex with biantennary N-glycan==
-<StructureSection load='5xfi' size='340' side='right' caption='[[5xfi]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='5xfi' size='340' side='right'caption='[[5xfi]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xfi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Calse Calse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xfi]] is a 2 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=5XFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XFI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.653&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xfh|5xfh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfi OCA], [http://pdbe.org/5xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfi RCSB], [http://www.ebi.ac.uk/pdbsum/5xfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfi ProSAT]</span></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=5xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfi OCA], [https://pdbe.org/5xfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xfi RCSB], [https://www.ebi.ac.uk/pdbsum/5xfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfi ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LECC_CALSE 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).<ref>PMID:14561768</ref> <ref>PMID:18266762</ref> <ref>PMID:26971576</ref> <ref>PMID:28973127</ref> <ref>PMID:9111143</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Calse]]
+[[Category: Calystegia sepium]]
-[[Category: Nagae, M]]
+[[Category: Large Structures]]
-[[Category: Yamaguchi, Y]]
+[[Category: Nagae M]]
-[[Category: Glycobiology]]
+[[Category: Yamaguchi Y]]
-[[Category: Jacalin-related lectin]]
-[[Category: Lectin]]
-[[Category: N-glycan]]
-[[Category: Sugar binding protein]]

5xfi

From Proteopedia

Current revision

Crystal structure of Calsepa lectin in complex with biantennary N-glycan

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox