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==CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN==
 
<StructureSection load='2vi6' size='340' side='right' caption='[[2vi6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
==Crystal Structure of the Nanog Homeodomain==
<StructureSection load='2vi6' size='340' side='right'caption='[[2vi6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2vi6]] is a 8 chain structure with 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]. <br>
<table><tr><td colspan='2'>[[2vi6]] is a 8 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VI6 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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]] 2.6&#8491;</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vi6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vi6 RCSB], [http://www.ebi.ac.uk/pdbsum/2vi6 PDBsum]</span></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=2vi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vi6 OCA], [https://pdbe.org/2vi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vi6 RCSB], [https://www.ebi.ac.uk/pdbsum/2vi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vi6 ProSAT]</span></td></tr>
<table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NANOG_MOUSE NANOG_MOUSE] Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal (PubMed:25825768). Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3'. Binds to the POU5F1/OCT4 promoter (By similarity). Able to autorepress its expression in differentiating (ES) cells: binds to its own promoter following interaction with ZNF281/ZFP281, leading to recruitment of the NuRD complex and subsequent repression of expression. When overexpressed, promotes cells to enter into S phase and proliferation.[UniProtKB:Q9H9S0]<ref>PMID:12787504</ref> <ref>PMID:12787505</ref> <ref>PMID:14728807</ref> <ref>PMID:15502159</ref> <ref>PMID:16518401</ref> <ref>PMID:16791199</ref> <ref>PMID:16801560</ref> <ref>PMID:21915945</ref> <ref>PMID:22988117</ref> <ref>PMID:25825768</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/2vi6_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/2vi6_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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=2vi6 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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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<ref>PMID:18177668</ref>
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<ref>PMID:18177668</ref>


From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 2vi6" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Jauch, R.]]
[[Category: Jauch R]]
[[Category: Kolatkar, P R.]]
[[Category: Kolatkar PR]]
[[Category: Ng, C K.L.]]
[[Category: Ng CKL]]
[[Category: Saitakendu, K S.]]
[[Category: Saitakendu KS]]
[[Category: Stevens, R C.]]
[[Category: Stevens RC]]
[[Category: Activator]]
[[Category: Developmental protein]]
[[Category: Dna-binding]]
[[Category: Homeobox]]
[[Category: Homeodomain]]
[[Category: Nanog]]
[[Category: Nucleus]]
[[Category: Repressor]]
[[Category: Transcription]]
[[Category: Transcription factor]]
[[Category: Transcription regulation]]

Latest revision as of 12:32, 6 November 2024

Crystal Structure of the Nanog HomeodomainCrystal Structure of the Nanog Homeodomain

Structural highlights

2vi6 is a 8 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NANOG_MOUSE Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal (PubMed:25825768). Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3'. Binds to the POU5F1/OCT4 promoter (By similarity). Able to autorepress its expression in differentiating (ES) cells: binds to its own promoter following interaction with ZNF281/ZFP281, leading to recruitment of the NuRD complex and subsequent repression of expression. When overexpressed, promotes cells to enter into S phase and proliferation.[UniProtKB:Q9H9S0][1] [2] [3] [4] [5] [6] [7] [8] [9] [10]

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, Takahashi K, Maruyama M, Maeda M, Yamanaka S. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell. 2003 May 30;113(5):631-42. PMID:12787504 doi:10.1016/s0092-8674(03)00393-3
  2. ↑ Chambers I, Colby D, Robertson M, Nichols J, Lee S, Tweedie S, Smith A. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell. 2003 May 30;113(5):643-55. PMID:12787505 doi:10.1016/s0092-8674(03)00392-1
  3. ↑ Pan GJ, Pei DQ. Identification of two distinct transactivation domains in the pluripotency sustaining factor nanog. Cell Res. 2003 Dec;13(6):499-502. PMID:14728807 doi:10.1038/sj.cr.7290193
  4. ↑ Pan G, Pei D. The stem cell pluripotency factor NANOG activates transcription with two unusually potent subdomains at its C terminus. J Biol Chem. 2005 Jan 14;280(2):1401-7. PMID:15502159 doi:10.1074/jbc.M407847200
  5. ↑ Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet. 2006 Apr;38(4):431-40. PMID:16518401 doi:10.1038/ng1760
  6. ↑ Silva J, Chambers I, Pollard S, Smith A. Nanog promotes transfer of pluripotency after cell fusion. Nature. 2006 Jun 22;441(7096):997-1001. PMID:16791199 doi:10.1038/nature04914
  7. ↑ Suzuki A, Raya Á, Kawakami Y, Morita M, Matsui T, Nakashima K, Gage FH, Rodríguez-Esteban C, Izpisúa Belmonte JC. Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells. Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10294-10299. PMID:16801560 doi:10.1073/pnas.0506945103
  8. ↑ Fidalgo M, Shekar PC, Ang YS, Fujiwara Y, Orkin SH, Wang J. Zfp281 functions as a transcriptional repressor for pluripotency of mouse embryonic stem cells. Stem Cells. 2011 Nov;29(11):1705-16. PMID:21915945 doi:10.1002/stem.736
  9. ↑ Fidalgo M, Faiola F, Pereira CF, Ding J, Saunders A, Gingold J, Schaniel C, Lemischka IR, Silva JC, Wang J. Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16202-7. PMID:22988117 doi:10.1073/pnas.1208533109
  10. ↑ Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ. Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. Proc Natl Acad Sci U S A. 2015 Mar 30. pii: 201502855. PMID:25825768 doi:http://dx.doi.org/10.1073/pnas.1502855112
  11. ↑ Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR. Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. J Mol Biol. 2008 Feb 22;376(3):758-70. Epub 2007 Dec 4. PMID:18177668 doi:10.1016/j.jmb.2007.11.091

2vi6, resolution 2.60Å

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