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1r5t

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[[Image:1r5t.gif|left|200px]]
 
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==The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast==
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The line below this paragraph, containing "STRUCTURE_1r5t", creates the "Structure Box" on the page.
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<StructureSection load='1r5t' size='340' side='right'caption='[[1r5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_1r5t| PDB=1r5t | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CDD_YEAST CDD_YEAST] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r5/1r5t_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1r5t ConSurf].
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<div style="clear:both"></div>
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'''The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast'''
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==See Also==
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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==About this Structure==
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1R5T is a [[Single protein]] structure of 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].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15148397 15148397]
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[[Category: Cytidine deaminase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Dance GSC]]
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[[Category: Dance, G S.C.]]
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[[Category: Smith HC]]
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[[Category: Smith, H C.]]
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[[Category: Sowden MP]]
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[[Category: Sowden, M P.]]
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[[Category: Torelli AT]]
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[[Category: Torelli, A T.]]
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[[Category: Wedekind JE]]
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[[Category: Wedekind, J E.]]
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[[Category: Xie K]]
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[[Category: Xie, K.]]
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[[Category: Apobec-1 related protein]]
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[[Category: Rna editing]]
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[[Category: Zinc dependent deaminase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:06:56 2008''
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Current revision

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast

PDB ID 1r5t

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