View source for 5y42


==Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina==
<StructureSection load='5y42' size='340' side='right'caption='[[5y42]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5y42]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichosanthes_anguina Trichosanthes anguina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y42 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]] 2.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5y42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y42 OCA], [https://pdbe.org/5y42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y42 RCSB], [https://www.ebi.ac.uk/pdbsum/5y42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y42 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SGSL_TRIAN SGSL_TRIAN] Seed lectin similar to type 2 ribosome-inactivating proteins (PubMed:23897472, PubMed:11375527). The Aalpha and Abeta chains constitute the rRNA glycosidase domain and the B chain the carbohydrate-binding lectin domain (PubMed:23897472). Is predicted to have no glycosidase activity and, hence, to be non-toxic, due to small changes in both the nucleotide binding and carbohydrate binding capabilities (PubMed:23897472, PubMed:11375527). Binds galactose and derivatives with a preference for the beta-anomeric forms (PubMed:8799450, PubMed:10877067). Binds prophyrins (PubMed:10877067). Has hemagglutinating activity towards rabbit and human erythrocytes (PubMed:8799450, PubMed:10877067).<ref>PMID:10877067</ref> <ref>PMID:11375527</ref> <ref>PMID:23897472</ref> <ref>PMID:8799450</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Snake gourd seed lectin (SGSL) is a non-toxic homologue of type II ribosome inactivating proteins (RIPs) which contain a catalytic domain and a lectin domain. Isothermal titration calorimetry (ITC) measurements of the interactions of the protein with LacNAc, Lac, Gal, Me-alpha-Gal were carried out and the crystal structures of the native protein and its complex with Lac were determined. The crystal structure of the Me-alpha-Gal complex has already been determined. While the crystal structure showed the presence of two-sugar binding sites, one on each of the two domains of the lectin chain, ITC measurements indicated the presence of only one binding site. In order to resolve this anomaly, Molecular Dynamics (MD) simulations were carried out on the native protein and on its complexes with Me-alpha-Gal and Lac. Simulations were also performed on the protein after reducing the inter-chain disulphide bridge between the two chains. The crystal structures and the simulations confirmed the robustness of the protein structure, irrespective of the presence or absence of the disulphide bridge. The simulations indicated that although two sites can bind sugar, only the ligand at one site is retained in a dynamic situation. The studies thus bring out the subtle relationship between binding and retention of the ligand.

Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study.,Chandran T, Sivaji N, Surolia A, Vijayan M Glycobiology. 2018 Aug 6. pii: 5067403. doi: 10.1093/glycob/cwy072. PMID:30099481<ref>PMID:30099481</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5y42" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Trichosanthes anguina]]
[[Category: Chandran T]]
[[Category: Vijayan M]]