1r5t: Difference between revisions

Revision as of 15:47, 21 February 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

1R5T is a Single protein structure of sequence from Saccharomyces cerevisiae with as ligand. Active as Cytidine deaminase, with EC number 3.5.4.5 Full crystallographic information is available from OCA.

ReferenceReference

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

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OCA

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-[[Image:1r5t.gif|left|200px]]<br /><applet load="1r5t" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1r5t.gif|left|200px]]<br /><applet load="1r5t" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1r5t, resolution 2.00&Aring;" />
 '''The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-R5T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R5T OCA].
+R5T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R5T OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Saccharomyces cerevisiae]]
 [[Category: Single protein]]
-[[Category: Dance, G.S.C.]]
+[[Category: Dance, G S.C.]]
-[[Category: Smith, H.C.]]
+[[Category: Smith, H C.]]
-[[Category: Sowden, M.P.]]
+[[Category: Sowden, M P.]]
-[[Category: Torelli, A.T.]]
+[[Category: Torelli, A T.]]
-[[Category: Wedekind, J.E.]]
+[[Category: Wedekind, J E.]]
 [[Category: Xie, K.]]
 [[Category: ZN]]
@@ Line 25: / Line 25: @@
 [[Category: zinc dependent deaminase]]
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