3ku0: Difference between revisions

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-{{Seed}}
-[[Image:3ku0.jpg|left|200px]]
-<!--
+==Structure of GAP31 with adenine at its binding pocket==
-The line below this paragraph, containing "STRUCTURE_3ku0", creates the "Structure Box" on the page.
+<StructureSection load='3ku0' size='340' side='right'caption='[[3ku0]], [[Resolution|resolution]] 1.90&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'>[[3ku0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Suregada_multiflora Suregada multiflora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KU0 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]] 1.9&#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_3ku0|  PDB=3ku0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ku0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ku0 OCA], [https://pdbe.org/3ku0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ku0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ku0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ku0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIPG_SURMU RIPG_SURMU]
+== 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/ku/3ku0_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=3ku0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.
-===Structure of GAP31 with adenine at its binding pocket===
+A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase--structural and modeling insight into its functions.,Li HG, Huang PL, Zhang D, Sun Y, Chen HC, Zhang J, Huang PL, Kong XP, Lee-Huang S Biochem Biophys Res Commun. 2010 Jan 1;391(1):340-5. Epub 2009 Nov 12. PMID:19913503<ref>PMID:19913503</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ku0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19913503}}, 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 19913503 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19913503}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-KU0 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Gelonium_multiflorum Gelonium multiflorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KU0 OCA].
+[[Category: Suregada multiflora]]
+[[Category: Kong X-P]]
-==Reference==
-<ref group="xtra">PMID:19913503</ref><references group="xtra"/>
-[[Category: Gelonium multiflorum]]
-[[Category: RRNA N-glycosylase]]
-[[Category: Kong, X P.]]
-[[Category: Disulfide bond]]
-[[Category: Glycoprotein]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Plant defense]]
-[[Category: Plant seed]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Toxin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 19:42:47 2010''