2vi6: Difference between revisions

Revision as of 19:46, 20 March 2008

, resolution 2.60Å

Coordinates:

CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN

OverviewOverview

The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.

About this StructureAbout this Structure

2VI6 is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog., Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR, J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:18177668

Page seeded by OCA on Thu Mar 20 18:46:48 2008

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OCA

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-[[Image:2vi6.jpg|left|200px]]<br /><applet load="2vi6" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2vi6.jpg|left|200px]]
-caption="2vi6, resolution 2.60&Aring;" />
-'''CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN'''<br />
+ {{Structure
+|PDB= 2vi6 |SIZE=350|CAPTION= <scene name='initialview01'>2vi6</scene>, resolution 2.60&Aring;
+|SITE=
+|LIGAND=
+|ACTIVITY=
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-VI6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VI6 OCA].
+VI6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VI6 OCA].
 ==Reference==
-Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog., Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR, J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18177668 18177668]
+Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog., Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR, J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18177668 18177668]
 [[Category: Mus musculus]]
 [[Category: Single protein]]
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 [[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:56:01 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:46:48 2008''