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[[Image:1r5t.gif|left|200px]]


{{Structure
==The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast==
|PDB= 1r5t |SIZE=350|CAPTION= <scene name='initialview01'>1r5t</scene>, resolution 2.00&Aring;
<StructureSection load='1r5t' size='340' side='right'caption='[[1r5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<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>
|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
|GENE= Cdd1p ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
<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>
|DOMAIN=
<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>
|RELATEDENTRY=[[1af2|1AF2]], [[1jtk|1JTK]]
</table>
|RESOURCES=<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.ebi.ac.uk/pdbsum/1r5t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r5t RCSB]</span>
== Function ==
}}
[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>
    <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/main_output.php?pdb_ID=1r5t ConSurf].
<div style="clear:both"></div>


'''The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast'''
==See Also==
 
*[[Deaminase 3D structures|Deaminase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
==About this Structure==
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].
 
==Reference==
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]
[[Category: Cytidine deaminase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Dance GSC]]
[[Category: Dance, G S.C.]]
[[Category: Smith HC]]
[[Category: Smith, H C.]]
[[Category: Sowden MP]]
[[Category: Sowden, M P.]]
[[Category: Torelli AT]]
[[Category: Torelli, A T.]]
[[Category: Wedekind JE]]
[[Category: Wedekind, J E.]]
[[Category: Xie K]]
[[Category: Xie, K.]]
[[Category: apobec-1 related protein]]
[[Category: rna editing]]
[[Category: zinc dependent deaminase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:23:39 2008''

Latest revision as of 11:20, 14 February 2024

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

Structural highlights

1r5t is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDD_YEAST This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1r5t, resolution 2.00Å

Drag the structure with the mouse to rotate

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OCA
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