|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina== | | ==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]] 2.90Å' scene=''> | + | <StructureSection load='5y42' size='340' side='right'caption='[[5y42]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y42]] is a 6 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y42 FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.9Å</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=5y42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y42 OCA], [http://pdbe.org/5y42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y42 RCSB], [http://www.ebi.ac.uk/pdbsum/5y42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y42 ProSAT]</span></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> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two beta-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL. However, the integrity of the three-dimensional structure of the catalytic component of the molecule is preserved. This is the first time that a three-chain RIP or RIP homologue has been observed. A thorough examination of the sequence and structure of the protein and of its interactions with the bound methyl-alpha-galactose indicate that the nontoxicity of SGSL results from a combination of changes in the catalytic and the carbohydrate-binding sites. Detailed analyses of the sequences of type II RIPs of known structure and their homologues with unknown structure provide valuable insights into the evolution of this class of proteins. They also indicate some variability in carbohydrate-binding sites, which appears to contribute to the different levels of toxicity exhibited by lectins from various sources.
| + | 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. |
| | | | |
| - | The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.,Sharma A, Pohlentz G, Bobbili KB, Jeyaprakash AA, Chandran T, Mormann M, Swamy MJ, Vijayan M Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1493-503. doi:, 10.1107/S0907444913010020. Epub 2013 Jul 18. PMID:23897472<ref>PMID:23897472</ref>
| + | 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | <div class="pdbe-citations 5y42" style="background-color:#fffaf0;"></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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Trichosanthes anguina]] | | [[Category: Trichosanthes anguina]] |
| - | [[Category: Chandran, T]] | + | [[Category: Chandran T]] |
| - | [[Category: Vijayan, M]] | + | [[Category: Vijayan M]] |
| - | [[Category: Beta-trefoil]]
| + | |
| - | [[Category: Lectin]]
| + | |
| - | [[Category: Plant protein]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4]
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Komath SS, Kenoth R, Giribabu L, Maiya BG, Swamy MJ. Fluorescence and absorption spectroscopic studies on the interaction of porphyrins with snake gourd (Trichosanthes anguina) seed lectin. J Photochem Photobiol B. 2000 Mar;55(1):49-55. PMID:10877067
- ↑ Manoj N, Jeyaprakash AA, Pratap JV, Komath SS, Kenoth R, Swamy MJ, Vijayan M. Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins. Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):912-4. Epub 2001 May 25. PMID:11375527
- ↑ Sharma A, Pohlentz G, Bobbili KB, Jeyaprakash AA, Chandran T, Mormann M, Swamy MJ, Vijayan M. The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs. Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1493-503. doi:, 10.1107/S0907444913010020. Epub 2013 Jul 18. PMID:23897472 doi:http://dx.doi.org/10.1107/S0907444913010020
- ↑ Komath SS, Nadimpalli SK, Swamy MJ. Purification in high yield and characterisation of the galactose-specific lectin from the seeds of snake gourd (Trichosanthes anguina). Biochem Mol Biol Int. 1996 May;39(2):243-52. PMID:8799450
- ↑ Chandran T, Sivaji N, Surolia A, Vijayan M. Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study. Glycobiology. 2018 Aug 6. pii: 5067403. doi: 10.1093/glycob/cwy072. PMID:30099481 doi:http://dx.doi.org/10.1093/glycob/cwy072
|
