3ku0: Difference between revisions

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-{{STRUCTURE_3ku0|  PDB=3ku0  |  SCENE=  }}
+==Structure of GAP31 with adenine at its binding pocket==
-===Structure of GAP31 with adenine at its binding pocket===
+<StructureSection load='3ku0' size='340' side='right' caption='[[3ku0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-{{ABSTRACT_PUBMED_19913503}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ku0]] is a 2 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KU0 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>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ktz|3ktz]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ku0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ku0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ku0 RCSB], [http://www.ebi.ac.uk/pdbsum/3ku0 PDBsum]</span></td></tr>
+</table>
+== 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/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/chain_selection.php?pdb_ID=2ata 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.
-==About this Structure==
+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>
-[[3ku0]] is a 2 chain structure with sequence 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].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:019913503</ref><references group="xtra"/><references/>
+</div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gelonium multiflorum]]
 [[Category: RRNA N-glycosylase]]
-[[Category: Kong, X P.]]
+[[Category: Kong, X P]]
 [[Category: Disulfide bond]]
 [[Category: Glycoprotein]]