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| ==1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES== | | ==1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES== |
| <StructureSection load='1lln' size='340' side='right' caption='[[1lln]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='1lln' size='340' side='right'caption='[[1lln]], [[Resolution|resolution]] 1.60Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[1lln]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LLN FirstGlance]. <br> | | <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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</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]] 1.6Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qcg|1qcg]]</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='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=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> |
| <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=1lln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lln OCA], [http://pdbe.org/1lln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lln RCSB], [http://www.ebi.ac.uk/pdbsum/1lln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lln ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RIP2_PHYAM RIP2_PHYAM]] Inhibits viral infection of plants. Inhibits protein synthesis in both prokaryotes and eukaryotes. | | [https://www.uniprot.org/uniprot/RIP2_PHYAM RIP2_PHYAM] Inhibits viral infection of plants. Inhibits protein synthesis in both prokaryotes and eukaryotes. |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| </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]. | | </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> | | <div style="clear:both"></div> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| 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.
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| 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:12754107<ref>PMID:12754107</ref>
| | ==See Also== |
| | | *[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]] |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 1lln" style="background-color:#fffaf0;"></div>
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| == References == | |
| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] |
| [[Category: Phytolacca americana]] | | [[Category: Phytolacca americana]] |
| [[Category: RRNA N-glycosylase]]
| | [[Category: Kurinov IV]] |
| [[Category: Kurinov, I V]] | | [[Category: Uckun FM]] |
| [[Category: Uckun, F M]] | |
| [[Category: Hydrolase]]
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| [[Category: Pokeweed antiviral protein]]
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| [[Category: Polynucleotide:adenosine]]
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| [[Category: Ribosome inactivating protein]]
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