1oum: Difference between revisions

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

OCA

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 ==M64V PNP +Talo==
-<StructureSection load='1oum' size='340' side='right' caption='[[1oum]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1oum' size='340' side='right'caption='[[1oum]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1oum]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OUM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1oum]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OUM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TAL:9-(6-DEOXY-ALPHA-L-TALOFURANOSYL)-6-METHYLPURINE'>TAL</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]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ecp|1ecp]], [[1a9o|1a9o]], [[1otx|1otx]], [[1oty|1oty]], [[1ou4|1ou4]], [[1ov6|1ov6]], [[1ovg|1ovg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TAL:9-(6-DEOXY-ALPHA-L-TALOFURANOSYL)-6-METHYLPURINE'>TAL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DEOD OR PUP OR B4384 OR Z5986 OR ECS5343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1oum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oum OCA], [https://pdbe.org/1oum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oum RCSB], [https://www.ebi.ac.uk/pdbsum/1oum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oum ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </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=1oum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oum OCA], [http://pdbe.org/1oum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oum RCSB], [http://www.ebi.ac.uk/pdbsum/1oum PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DEOD_ECOLI DEOD_ECOLI]] Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.[HAMAP-Rule:MF_01627]
+[https://www.uniprot.org/uniprot/DEOD_ECOLI DEOD_ECOLI] Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.[HAMAP-Rule:MF_01627]
 == 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/ou/1oum_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ou/1oum_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=1oum ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Activation of prodrugs by Escherichia coli purine nucleoside phosphorylase (PNP) provides a method for selectively killing tumor cells expressing a transfected PNP gene. This gene therapy approach requires matching a prodrug and a known enzymatic activity present only in tumor cells. The specificity of the method relies on avoiding prodrug cleavage by enzymes already present in the host cells or the intestinal flora. Using crystallographic and computer modeling methods as guides, we have redesigned E. coli PNP to cleave new prodrug substrates more efficiently than does the wild-type enzyme. In particular, the M64V PNP mutant cleaves 9-(6-deoxy-alpha-L-talofuranosyl)-6-methylpurine with a kcat/Km over 100 times greater than for native E. coli PNP. In a xenograft tumor experiment, this compound caused regression of tumors expressing the M64V PNP gene.
-Designer gene therapy using an Escherichia coli purine nucleoside phosphorylase/prodrug system.,Bennett EM, Anand R, Allan PW, Hassan AE, Hong JS, Levasseur DN, McPherson DT, Parker WB, Secrist JA 3rd, Sorscher EJ, Townes TM, Waud WR, Ealick SE Chem Biol. 2003 Dec;10(12):1173-81. PMID:14700625<ref>PMID:14700625</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1oum" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Purine nucleoside phosphorylase|Purine nucleoside phosphorylase]]
+*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Purine-nucleoside phosphorylase]]
+[[Category: Large Structures]]
-[[Category: Allan, P W]]
+[[Category: Allan PW]]
-[[Category: Anand, R]]
+[[Category: Anand R]]
-[[Category: Bennett, E M]]
+[[Category: Bennett EM]]
-[[Category: Ealick, S E]]
+[[Category: Ealick SE]]
-[[Category: Hassan, A E]]
+[[Category: Hassan AE]]
-[[Category: McPherson, D T]]
+[[Category: McPherson DT]]
-[[Category: Parker, W B]]
+[[Category: Parker WB]]
-[[Category: Secrist, J A]]
+[[Category: Secrist JA]]
-[[Category: Sorscher, E J]]
+[[Category: Sorscher EJ]]
-[[Category: M64v]]
-[[Category: Pnp]]
-[[Category: Talo]]
-[[Category: Transferase]]