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| | ==Crystal structure of Orysata lectin in complex with biantennary N-glycan== | | ==Crystal structure of Orysata lectin in complex with biantennary N-glycan== |
| - | <StructureSection load='5xfh' size='340' side='right' caption='[[5xfh]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='5xfh' size='340' side='right'caption='[[5xfh]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5xfh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xfh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XFH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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]] 1.903Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xfi|5xfi]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SALT, ML, Os01g0348900, LOC_Os01g24710, B1051E10.18, P0440D10.39 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=5xfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfh OCA], [https://pdbe.org/5xfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xfh RCSB], [https://www.ebi.ac.uk/pdbsum/5xfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfh ProSAT]</span></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=5xfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfh OCA], [http://pdbe.org/5xfh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfh RCSB], [http://www.ebi.ac.uk/pdbsum/5xfh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SALT_ORYSJ SALT_ORYSJ] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Japanese rice]] | + | [[Category: Large Structures]] |
| - | [[Category: Nagae, M]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Yamaguchi, Y]] | + | [[Category: Nagae M]] |
| - | [[Category: Glycobiology]] | + | [[Category: Yamaguchi Y]] |
| - | [[Category: Jacalin-related lectin]]
| + | |
| - | [[Category: Lectin]]
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| - | [[Category: N-glycan]]
| + | |
| - | [[Category: Sugar binding protein]]
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| Structural highlights
Function
SALT_ORYSJ
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
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