3le7

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (02:04, 21 November 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3le7.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of PD-L1 from P. dioica in complex with adenine==
-
The line below this paragraph, containing "STRUCTURE_3le7", creates the "Structure Box" on the page.
+
<StructureSection load='3le7' size='340' side='right'caption='[[3le7]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</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>
-
{{STRUCTURE_3le7| PDB=3le7 | SCENE= }}
+
<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>
 +
</table>
 +
== Function ==
 +
[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 ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<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/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3le7 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===Crystal structure of PD-L1 from P. dioica in complex with adenine===
+
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<ref>PMID:20174685</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3le7" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20174685}}, adds the Publication Abstract to the page
+
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20174685 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20174685}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3LE7 is a 2 chains structure with sequences 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].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:20174685</ref><references group="xtra"/>
+
[[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]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 09:44:24 2010''
+

Current revision

Crystal structure of PD-L1 from P. dioica in complex with adenine

PDB ID 3le7

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools