1lln: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1lln.gif|left|200px]]<br />
-<applet load="1lln" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1lln, resolution 1.60&Aring;" />
-'''1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES'''<br />
-==Overview==
+==1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES==
-Pokeweed antiviral protein III (PAP-III), a naturally occurring protein, isolated from late summer leaves of the pokeweed plant (Phytolacca, americana), has potent anti-HIV activity by an as yet undetermined, molecular mechanism. PAP-III belongs to a family of ribosome-inactivating, proteins that catalytically deadenylate ribosomal and viral RNA. The, chemical modification of PAP-III by reductive methylation of its lysine, residues significantly improved the crystal quality for X-ray diffraction, studies. Trigonal crystals of the modified PAP-III, with unit cell, parameters a=b=80.47A, c=76.21A, were obtained using 30% PEG400 as the, precipitant. These crystals contained one enzyme molecule per asymmetric, unit and diffracted up to 1.5A, when exposed to a synchrotron source. Here, we report the X-ray crystal structure of PAP-III at 1.6A resolution, which, was solved by molecular replacement using the homology model of PAP-III as, a search model. The fold typical of other ribosome-inactivating proteins, is conserved, despite several differences on the surface and in the loop, regions. Residues Tyr(69), Tyr(117), Glu(172), and Arg(175) are expected, to define the active site of PAP-III. Molecular modeling studies of the, interactions of PAP-III and PAP-I with a single-stranded RNA heptamer, predicted a more potent anti-HIV activity for PAP-III due to its unique, surface topology and more favorable charge distribution in its 20A-long, RNA binding active center cleft. In accordance with the predictions of the, modeling studies, PAP-III was more potent than PAP-I in depurinating HIV-1, RNA.
+<StructureSection load='1lln' size='340' side='right'caption='[[1lln]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1lln]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_americana Phytolacca americana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LLN 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</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=1lln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lln OCA], [https://pdbe.org/1lln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lln RCSB], [https://www.ebi.ac.uk/pdbsum/1lln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lln ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIP2_PHYAM RIP2_PHYAM] Inhibits viral infection of plants. Inhibits protein synthesis in both prokaryotes and eukaryotes.
+== 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/ll/1lln_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1lln ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-LLN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Phytolacca_americana Phytolacca americana]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LLN OCA].
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-High resolution X-ray structure of potent anti-HIV pokeweed antiviral protein-III., Kurinov IV, Uckun FM, Biochem Pharmacol. 2003 May 15;65(10):1709-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12754107 12754107]
+[[Category: Large Structures]]
 [[Category: Phytolacca americana]]
-[[Category: Single protein]]
+[[Category: Kurinov IV]]
-[[Category: rRNA N-glycosylase]]
+[[Category: Uckun FM]]
-[[Category: Kurinov, I.V.]]
-[[Category: Uckun, F.M.]]
-[[Category: pokeweed antiviral protein]]
-[[Category: polynucleotide:adenosine]]
-[[Category: ribosome inactivating protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 14:17:19 2007''