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| | ==Crystal structure of PD-L1 from P. dioica in complex with adenine== | | ==Crystal structure of PD-L1 from P. dioica in complex with adenine== |
| - | <StructureSection load='3le7' size='340' side='right' caption='[[3le7]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='3le7' size='340' side='right'caption='[[3le7]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3le7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LE7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LE7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3le7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LE7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3h5k|3h5k]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=3le7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3le7 OCA], [https://pdbe.org/3le7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3le7 RCSB], [https://www.ebi.ac.uk/pdbsum/3le7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3le7 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=3le7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3le7 OCA], [http://pdbe.org/3le7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3le7 RCSB], [http://www.ebi.ac.uk/pdbsum/3le7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3le7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RIPL1_PHYDI RIPL1_PHYDI]] Inhibits protein synthesis. Cleaves supercoiled pBR322 dsDNA.<ref>PMID:10213004</ref> <ref>PMID:15899692</ref> | + | [https://www.uniprot.org/uniprot/RIPL1_PHYDI RIPL1_PHYDI] Inhibits protein synthesis. Cleaves supercoiled pBR322 dsDNA.<ref>PMID:10213004</ref> <ref>PMID:15899692</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3le7_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/le/3le7_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | </div> | | </div> |
| | <div class="pdbe-citations 3le7" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3le7" 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: Phytolacca dioica]] | | [[Category: Phytolacca dioica]] |
| - | [[Category: RRNA N-glycosylase]]
| + | [[Category: Berisio R]] |
| - | [[Category: Berisio, R]] | + | [[Category: Ruggiero A]] |
| - | [[Category: Ruggiero, A]] | + | |
| - | [[Category: Adenine]]
| + | |
| - | [[Category: Disulfide bond]]
| + | |
| - | [[Category: Glycoprotein]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Plant defense]]
| + | |
| - | [[Category: Protein synthesis inhibitor]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Toxin]]
| + | |
| Structural highlights
Function
RIPL1_PHYDI Inhibits protein synthesis. Cleaves supercoiled pBR322 dsDNA.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
N-glycosylation is one of the major naturally occurring covalent co-translational modifications of proteins in plants, being involved in proteins structure, folding, stability and biological activity. In the present work the influence of carbohydrate moieties on the structure-function relationships of type 1 ribosome-inactivating proteins (RIPs) was investigated. To this aim, PD-Ls, RIPs isolated from Phytolacca dioica L. leaves, differing for their glycosylation degree, were used as an experimental system. In particular, comparative structural and biological analyses were performed using native and unglycosylated recombinant PD-L1, the most glycosylated P. dioica RIP isoform. The glycans influence on protein synthesis inhibition and adenine polynucleotide glycosidase activity was investigated. The interaction with adenine, the product of the de-adenylation reaction, was also investigated for native and recombinant PD-L1 by fluorescence spectroscopy. Furthermore, the crystal structure of PD-L1 in complex with adenine was determined. Our data confirm that the absence of glycan moieties did not affect the biological activity in terms of protein synthesis inhibition. However, the removal of carbohydrate chains significantly increased the deadenylation capability, likely as a consequence of the increased accessibility of substrates to the active site pocket. Furthermore, preliminary data on cellular uptake showed that all PD-L isoforms were internalized and, for the first time, that the vesicular distribution within cells could be influenced by the protein glycosylation degree.
The role of the glycan moiety on the structure-function relationships of PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves.,Severino V, Chambery A, Di Maro A, Marasco D, Ruggiero A, Berisio R, Giansanti F, Ippoliti R, Parente A Mol Biosyst. 2010 Mar;6(3):570-9. Epub 2010 Jan 21. PMID:20174685[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Di Maro A, Valbonesi P, Bolognesi A, Stirpe F, De Luca P, Siniscalco Gigliano G, Gaudio L, Delli Bovi P, Ferranti P, Malorni A, Parente A. Isolation and characterization of four type-1 ribosome-inactivating proteins, with polynucleotide:adenosine glycosidase activity, from leaves of Phytolacca dioica L. Planta. 1999 Mar;208(1):125-31. PMID:10213004
- ↑ Aceto S, Di Maro A, Conforto B, Siniscalco GG, Parente A, Delli Bovi P, Gaudio L. Nicking activity on pBR322 DNA of ribosome inactivating proteins from Phytolacca dioica L. leaves. Biol Chem. 2005 Apr;386(4):307-17. PMID:15899692 doi:10.1515/BC.2005.037
- ↑ Severino V, Chambery A, Di Maro A, Marasco D, Ruggiero A, Berisio R, Giansanti F, Ippoliti R, Parente A. The role of the glycan moiety on the structure-function relationships of PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves. Mol Biosyst. 2010 Mar;6(3):570-9. Epub 2010 Jan 21. PMID:20174685 doi:10.1039/b919801f
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