5xfi

From Proteopedia

(Difference between revisions)

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 3: / Line 3: @@
 <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://proteopedia.org/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" 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=SO4:SULFATE+ION'>SO4</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></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://proteopedia.org/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: Large Structures]]
-[[Category: Nagae, M]]
+[[Category: Nagae M]]
-[[Category: Yamaguchi, Y]]
+[[Category: Yamaguchi Y]]
-[[Category: Glycobiology]]
-[[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?)

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