3kvh: Difference between revisions

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==Crystal structure of human protein syndesmos (NUDT16-like protein)==
==Crystal structure of human protein syndesmos (NUDT16-like protein)==
<StructureSection load='3kvh' size='340' side='right' caption='[[3kvh]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3kvh' size='340' side='right'caption='[[3kvh]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3kvh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVH FirstGlance]. <br>
<table><tr><td colspan='2'>[[3kvh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KVH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 1.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDT16L1, SDOS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvh OCA], [http://pdbe.org/3kvh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvh RCSB], [http://www.ebi.ac.uk/pdbsum/3kvh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvh ProSAT]</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=3kvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvh OCA], [https://pdbe.org/3kvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kvh RCSB], [https://www.ebi.ac.uk/pdbsum/3kvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SDOS_HUMAN SDOS_HUMAN]] Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors (By similarity). Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA.  
[https://www.uniprot.org/uniprot/TIRR_HUMAN TIRR_HUMAN] Key regulator of TP53BP1 required to stabilize TP53BP1 and regulate its recruitment to chromatin (PubMed:28241136). In absence of DNA damage, interacts with the tandem Tudor-like domain of TP53BP1, masking the region that binds histone H4 dimethylated at 'Lys-20' (H4K20me2), thereby preventing TP53BP1 recruitment to chromatin and maintaining TP53BP1 localization to the nucleus (PubMed:28241136). Following DNA damage, ATM-induced phosphorylation of TP53BP1 and subsequent recruitment of RIF1 leads to dissociate NUDT16L1/TIRR from TP53BP1, unmasking the tandem Tudor-like domain and allowing recruitment of TP53BP1 to DNA double strand breaks (DSBs) (PubMed:28241136). Binds U8 snoRNA (PubMed:18820299).<ref>PMID:18820299</ref> <ref>PMID:28241136</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3kvh 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=3kvh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Arrowsmith, C H]]
[[Category: Large Structures]]
[[Category: Berg, S Van Den]]
[[Category: Arrowsmith CH]]
[[Category: Berglund, H]]
[[Category: Berglund H]]
[[Category: Bountra, C]]
[[Category: Bountra C]]
[[Category: Collins, R]]
[[Category: Collins R]]
[[Category: Edwards, A M]]
[[Category: Edwards AM]]
[[Category: Flodin, S]]
[[Category: Flodin S]]
[[Category: Flores, A]]
[[Category: Flores A]]
[[Category: Graslund, S]]
[[Category: Graslund S]]
[[Category: Hammarstrom, M]]
[[Category: Hammarstrom M]]
[[Category: Johansson, A]]
[[Category: Johansson A]]
[[Category: Johansson, I]]
[[Category: Johansson I]]
[[Category: Kallas, A]]
[[Category: Kallas A]]
[[Category: Karlberg, T]]
[[Category: Karlberg T]]
[[Category: Kotenyova, T]]
[[Category: Kotenyova T]]
[[Category: Kotzsch, A]]
[[Category: Kotzsch A]]
[[Category: Kraulis, P]]
[[Category: Kraulis P]]
[[Category: Moche, M]]
[[Category: Moche M]]
[[Category: Nielsen, T K]]
[[Category: Nielsen TK]]
[[Category: Nordlund, P]]
[[Category: Nordlund P]]
[[Category: Nyman, T]]
[[Category: Nyman T]]
[[Category: Persson, C]]
[[Category: Persson C]]
[[Category: Roos, A K]]
[[Category: Roos AK]]
[[Category: Structural genomic]]
[[Category: Schuler H]]
[[Category: Schuler, H]]
[[Category: Schutz P]]
[[Category: Schutz, P]]
[[Category: Siponen MI]]
[[Category: Siponen, M I]]
[[Category: Thorsell AG]]
[[Category: Thorsell, A G]]
[[Category: Tresaugues L]]
[[Category: Tresaugues, L]]
[[Category: Van Den Berg S]]
[[Category: Weigelt, J]]
[[Category: Weigelt J]]
[[Category: Welin, M]]
[[Category: Welin M]]
[[Category: Wisniewska, M]]
[[Category: Wisniewska M]]
[[Category: Nudix]]
[[Category: Nudt16-like]]
[[Category: Nudt16l1]]
[[Category: Rna binding protein]]
[[Category: Rna degradation]]
[[Category: Rna regulation]]
[[Category: Rna-binding]]
[[Category: Sgc]]
[[Category: Syndesmo]]

Latest revision as of 11:24, 6 September 2023

Crystal structure of human protein syndesmos (NUDT16-like protein)Crystal structure of human protein syndesmos (NUDT16-like protein)

Structural highlights

3kvh is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TIRR_HUMAN Key regulator of TP53BP1 required to stabilize TP53BP1 and regulate its recruitment to chromatin (PubMed:28241136). In absence of DNA damage, interacts with the tandem Tudor-like domain of TP53BP1, masking the region that binds histone H4 dimethylated at 'Lys-20' (H4K20me2), thereby preventing TP53BP1 recruitment to chromatin and maintaining TP53BP1 localization to the nucleus (PubMed:28241136). Following DNA damage, ATM-induced phosphorylation of TP53BP1 and subsequent recruitment of RIF1 leads to dissociate NUDT16L1/TIRR from TP53BP1, unmasking the tandem Tudor-like domain and allowing recruitment of TP53BP1 to DNA double strand breaks (DSBs) (PubMed:28241136). Binds U8 snoRNA (PubMed:18820299).[1] [2]

Evolutionary Conservation

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

References

  1. ↑ Taylor MJ, Peculis BA. Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme. Nucleic Acids Res. 2008 Oct;36(18):6021-34. doi: 10.1093/nar/gkn605. Epub 2008, Sep 27. PMID:18820299 doi:http://dx.doi.org/10.1093/nar/gkn605
  2. ↑ Drane P, Brault ME, Cui G, Meghani K, Chaubey S, Detappe A, Parnandi N, He Y, Zheng XF, Botuyan MV, Kalousi A, Yewdell WT, Munch C, Harper JW, Chaudhuri J, Soutoglou E, Mer G, Chowdhury D. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature. 2017 Mar 9;543(7644):211-216. doi: 10.1038/nature21358. Epub 2017 Feb 27. PMID:28241136 doi:http://dx.doi.org/10.1038/nature21358

3kvh, resolution 1.70Å

Drag the structure with the mouse to rotate

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