1r5t: Difference between revisions

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 ==The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast==
-<StructureSection load='1r5t' size='340' side='right' caption='[[1r5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1r5t' size='340' side='right'caption='[[1r5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r5t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R5T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r5t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R5T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1af2|1af2]], [[1jtk|1jtk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cdd1p ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=1r5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r5t OCA], [https://pdbe.org/1r5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r5t RCSB], [https://www.ebi.ac.uk/pdbsum/1r5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r5t 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/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] </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=1r5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r5t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r5t RCSB], [http://www.ebi.ac.uk/pdbsum/1r5t PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CDD_YEAST CDD_YEAST]] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
+[https://www.uniprot.org/uniprot/CDD_YEAST CDD_YEAST] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
 == 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/r5/1r5t_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r5/1r5t_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].
+</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=1r5t ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of APOBEC-1 that exhibits cytidine deaminase and RNA-editing activity. Here, we present the crystal structure of CDD1 at 2.0-A resolution and its use in comparative modeling of APOBEC-1 and AID. The models explain dimerization and the need for trans-acting loops that contribute to active site formation. Substrate selectivity appears to be regulated by a central active site "flap" whose size and flexibility accommodate large substrates in contrast to deaminases of pyrimidine metabolism that bind only small nucleosides or free bases. Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets.
-The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.,Xie K, Sowden MP, Dance GS, Torelli AT, Smith HC, Wedekind JE Proc Natl Acad Sci U S A. 2004 May 25;101(21):8114-9. Epub 2004 May 17. PMID:15148397<ref>PMID:15148397</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Deaminase|Deaminase]]
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cytidine deaminase]]
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Dance, G S.C]]
+[[Category: Dance GSC]]
-[[Category: Smith, H C]]
+[[Category: Smith HC]]
-[[Category: Sowden, M P]]
+[[Category: Sowden MP]]
-[[Category: Torelli, A T]]
+[[Category: Torelli AT]]
-[[Category: Wedekind, J E]]
+[[Category: Wedekind JE]]
-[[Category: Xie, K]]
+[[Category: Xie K]]
-[[Category: Apobec-1 related protein]]
-[[Category: Hydrolase]]
-[[Category: Rna editing]]
-[[Category: Zinc dependent deaminase]]