5yzp

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of p204 HINa domain

Structural highlights

5yzp is a 1 chain structure with sequence from Mus musculus domesticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.581Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IFI4_MOUSE Inhibits the transcription of ribosomal RNA. May inhibit DNA binding by UBTF. Inhibits cell growth via p53/TP53 and RB1-dependent and independent pathways. Acts as a coactivator of RUNX2 during osteogenesis. May be involved in macrophage differentiation. Enables skeletal muscle and cardiac myocyte differentiation by sequestring Id proteins in the cytosol and promoting their ubiquitination and subsequent degradation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins. Moreover, we obtained the crystal structure of p204 HINab domain in complex with dsDNA and provided insights into the dsDNA binding mode. p204 HINab binds dsDNA mainly through alpha2 helix of HINa and HINb, and the linker between them, revealing a similar HIN:DNA binding mode. Both HINa and HINb are vital for HINab recognition of dsDNA, as confirmed by fluorescence polarization assays. Furthermore, a HINa dimerization interface was observed in structures of p204 HINa and HINab:dsDNA complex, which is involved in binding dsDNA. The linker between HINa and HINb reveals dynamic flexibility in solution and changes its direction at approximately 90 degrees angle in comparison with crystal structure of HINab:dsDNA complex. These structural information provide insights into the mechanism of DNA recognition by different HIN domains, and shed light on the unique roles of two HIN domains in activating the IFI16/p204 signaling pathway.

Structural mechanism of DNA recognition by the p204 HIN domain.,Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P, Unterholzner L, Xiao TS, Jin T Nucleic Acids Res. 2021 Feb 22. pii: 6146633. doi: 10.1093/nar/gkab076. PMID:33619523^[8]

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

References

↑ Liu CJ, Wang H, Lengyel P. The interferon-inducible nucleolar p204 protein binds the ribosomal RNA-specific UBF1 transcription factor and inhibits ribosomal RNA transcription. EMBO J. 1999 May 17;18(10):2845-54. PMID:10329630 doi:http://dx.doi.org/10.1093/emboj/18.10.2845
↑ Liu CJ, Ding B, Wang H, Lengyel P. The MyoD-inducible p204 protein overcomes the inhibition of myoblast differentiation by Id proteins. Mol Cell Biol. 2002 May;22(9):2893-905. PMID:11940648
↑ Liu CJ, Chang E, Yu J, Carlson CS, Prazak L, Yu XP, Ding B, Lengyel P, Di Cesare PE. The interferon-inducible p204 protein acts as a transcriptional coactivator of Cbfa1 and enhances osteoblast differentiation. J Biol Chem. 2005 Jan 28;280(4):2788-96. doi: 10.1074/jbc.M412604200. Epub 2004, Nov 19. PMID:15557274 doi:http://dx.doi.org/10.1074/jbc.M412604200
↑ Dauffy J, Mouchiroud G, Bourette RP. The interferon-inducible gene, Ifi204, is transcriptionally activated in response to M-CSF, and its expression favors macrophage differentiation in myeloid progenitor cells. J Leukoc Biol. 2006 Jan;79(1):173-83. Epub 2005 Oct 21. PMID:16244109 doi:http://dx.doi.org/jlb.0205083
↑ Asefa B, Dermott JM, Kaldis P, Stefanisko K, Garfinkel DJ, Keller JR. p205, a potential tumor suppressor, inhibits cell proliferation via multiple pathways of cell cycle regulation. FEBS Lett. 2006 Feb 20;580(5):1205-14. Epub 2006 Jan 20. PMID:16458891 doi:http://dx.doi.org/10.1016/j.febslet.2006.01.032
↑ Ding B, Liu CJ, Huang Y, Hickey RP, Yu J, Kong W, Lengyel P. p204 is required for the differentiation of P19 murine embryonal carcinoma cells to beating cardiac myocytes: its expression is activated by the cardiac Gata4, Nkx2.5, and Tbx5 proteins. J Biol Chem. 2006 May 26;281(21):14882-92. doi: 10.1074/jbc.M511747200. Epub 2006, Mar 22. PMID:16556595 doi:http://dx.doi.org/10.1074/jbc.M511747200
↑ Ding B, Liu CJ, Huang Y, Yu J, Kong W, Lengyel P. p204 protein overcomes the inhibition of the differentiation of P19 murine embryonal carcinoma cells to beating cardiac myocytes by Id proteins. J Biol Chem. 2006 May 26;281(21):14893-906. doi: 10.1074/jbc.M511748200. Epub, 2006 Mar 22. PMID:16556596 doi:http://dx.doi.org/10.1074/jbc.M511748200
↑ Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P, Unterholzner L, Xiao TS, Jin T. Structural mechanism of DNA recognition by the p204 HIN domain. Nucleic Acids Res. 2021 Feb 22. pii: 6146633. doi: 10.1093/nar/gkab076. PMID:33619523 doi:http://dx.doi.org/10.1093/nar/gkab076

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yzp"

Categories: Large Structures | Mus musculus domesticus | Jin T

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5yzp is ON HOLD
+==Crystal structure of p204 HINa domain==
+<StructureSection load='5yzp' size='340' side='right'caption='[[5yzp]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5yzp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus_domesticus Mus musculus domesticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZP FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.581&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=5yzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzp OCA], [https://pdbe.org/5yzp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzp RCSB], [https://www.ebi.ac.uk/pdbsum/5yzp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IFI4_MOUSE IFI4_MOUSE] Inhibits the transcription of ribosomal RNA. May inhibit DNA binding by UBTF. Inhibits cell growth via p53/TP53 and RB1-dependent and independent pathways. Acts as a coactivator of RUNX2 during osteogenesis. May be involved in macrophage differentiation. Enables skeletal muscle and cardiac myocyte differentiation by sequestring Id proteins in the cytosol and promoting their ubiquitination and subsequent degradation.<ref>PMID:10329630</ref> <ref>PMID:11940648</ref> <ref>PMID:15557274</ref> <ref>PMID:16244109</ref> <ref>PMID:16458891</ref> <ref>PMID:16556595</ref> <ref>PMID:16556596</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins. Moreover, we obtained the crystal structure of p204 HINab domain in complex with dsDNA and provided insights into the dsDNA binding mode. p204 HINab binds dsDNA mainly through alpha2 helix of HINa and HINb, and the linker between them, revealing a similar HIN:DNA binding mode. Both HINa and HINb are vital for HINab recognition of dsDNA, as confirmed by fluorescence polarization assays. Furthermore, a HINa dimerization interface was observed in structures of p204 HINa and HINab:dsDNA complex, which is involved in binding dsDNA. The linker between HINa and HINb reveals dynamic flexibility in solution and changes its direction at approximately 90 degrees angle in comparison with crystal structure of HINab:dsDNA complex. These structural information provide insights into the mechanism of DNA recognition by different HIN domains, and shed light on the unique roles of two HIN domains in activating the IFI16/p204 signaling pathway.
-Authors: Jin, T.
+Structural mechanism of DNA recognition by the p204 HIN domain.,Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P, Unterholzner L, Xiao TS, Jin T Nucleic Acids Res. 2021 Feb 22. pii: 6146633. doi: 10.1093/nar/gkab076. PMID:33619523<ref>PMID:33619523</ref>
-Description: Crystal structure of p204 HINa domain
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Jin, T]]
+<div class="pdbe-citations 5yzp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mus musculus domesticus]]
+[[Category: Jin T]]

5yzp

From Proteopedia

Current revision

Crystal structure of p204 HINa domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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