4um2

From Proteopedia

(Difference between revisions)

Revision as of 08:28, 22 March 2023

Crystal structure of the TPR domain of SMG6

Structural highlights

4um2 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.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EST1A_HUMAN Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5'-(GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER).^[1] ^[2] ^[3] ^[4] ^[5] Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA), but not ssDNA or dsRNA.^[6] ^[7] ^[8] ^[9] ^[10]

Publication Abstract from PubMed

Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that recognizes mRNAs with premature stop codons and targets them for rapid degradation. Evidence from previous studies has converged on UPF1 as the central NMD factor. In human cells, the SMG1 kinase phosphorylates UPF1 at the N-terminal and C-terminal tails, in turn allowing the recruitment of the NMD factors SMG5, SMG6 and SMG7. To understand the molecular mechanisms, we recapitulated these steps of NMD in vitro using purified components. We find that a short C-terminal segment of phosphorylated UPF1 containing the last two Ser-Gln motifs is recognized by the heterodimer of SMG5 and SMG7 14-3-3-like proteins. In contrast, the SMG6 14-3-3-like domain is a monomer. The crystal structure indicates that the phosphoserine binding site of the SMG6 14-3-3-like domain is similar to that of SMG5 and can mediate a weak phospho-dependent interaction with UPF1. The dominant SMG6-UPF1 interaction is mediated by a low-complexity region bordering the 14-3-3-like domain of SMG6 and by the helicase domain and C-terminal tail of UPF1. This interaction is phosphorylation independent. Our study demonstrates that SMG5-SMG7 and SMG6 exhibit different and non-overlapping modes of UPF1 recognition, thus pointing at distinguished roles in integrating the complex NMD interaction network.

Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6.,Chakrabarti S, Bonneau F, Schussler S, Eppinger E, Conti E Nucleic Acids Res. 2014 Jul 10. pii: gku578. PMID:25013172^[11]

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

References

↑ Reichenbach P, Hoss M, Azzalin CM, Nabholz M, Bucher P, Lingner J. A human homolog of yeast Est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr Biol. 2003 Apr 1;13(7):568-74. PMID:12676087
↑ Snow BE, Erdmann N, Cruickshank J, Goldman H, Gill RM, Robinson MO, Harrington L. Functional conservation of the telomerase protein Est1p in humans. Curr Biol. 2003 Apr 15;13(8):698-704. PMID:12699629
↑ Huntzinger E, Kashima I, Fauser M, Sauliere J, Izaurralde E. SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA. 2008 Dec;14(12):2609-17. doi: 10.1261/rna.1386208. Epub 2008 Oct 30. PMID:18974281 doi:http://dx.doi.org/10.1261/rna.1386208
↑ Eberle AB, Lykke-Andersen S, Muhlemann O, Jensen TH. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat Struct Mol Biol. 2009 Jan;16(1):49-55. doi: 10.1038/nsmb.1530. Epub 2008 Dec , 7. PMID:19060897 doi:http://dx.doi.org/10.1038/nsmb.1530
↑ Glavan F, Behm-Ansmant I, Izaurralde E, Conti E. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J. 2006 Nov 1;25(21):5117-25. Epub 2006 Oct 19. PMID:17053788
↑ Reichenbach P, Hoss M, Azzalin CM, Nabholz M, Bucher P, Lingner J. A human homolog of yeast Est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr Biol. 2003 Apr 1;13(7):568-74. PMID:12676087
↑ Snow BE, Erdmann N, Cruickshank J, Goldman H, Gill RM, Robinson MO, Harrington L. Functional conservation of the telomerase protein Est1p in humans. Curr Biol. 2003 Apr 15;13(8):698-704. PMID:12699629
↑ Huntzinger E, Kashima I, Fauser M, Sauliere J, Izaurralde E. SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA. 2008 Dec;14(12):2609-17. doi: 10.1261/rna.1386208. Epub 2008 Oct 30. PMID:18974281 doi:http://dx.doi.org/10.1261/rna.1386208
↑ Eberle AB, Lykke-Andersen S, Muhlemann O, Jensen TH. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat Struct Mol Biol. 2009 Jan;16(1):49-55. doi: 10.1038/nsmb.1530. Epub 2008 Dec , 7. PMID:19060897 doi:http://dx.doi.org/10.1038/nsmb.1530
↑ Glavan F, Behm-Ansmant I, Izaurralde E, Conti E. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J. 2006 Nov 1;25(21):5117-25. Epub 2006 Oct 19. PMID:17053788
↑ Chakrabarti S, Bonneau F, Schussler S, Eppinger E, Conti E. Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6. Nucleic Acids Res. 2014 Jul 10. pii: gku578. PMID:25013172 doi:http://dx.doi.org/10.1093/nar/gku578

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4um2"

@@ Line 3: / Line 3: @@
 <StructureSection load='4um2' size='340' side='right'caption='[[4um2]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4um2]] 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=4UM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UM2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4um2]] 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=4UM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UM2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4um2 OCA], [http://pdbe.org/4um2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4um2 RCSB], [http://www.ebi.ac.uk/pdbsum/4um2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4um2 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=4um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4um2 OCA], [https://pdbe.org/4um2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4um2 RCSB], [https://www.ebi.ac.uk/pdbsum/4um2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4um2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/EST1A_HUMAN EST1A_HUMAN]] Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5'-(GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER).<ref>PMID:12676087</ref> <ref>PMID:12699629</ref> <ref>PMID:18974281</ref> <ref>PMID:19060897</ref> <ref>PMID:17053788</ref>   Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA), but not ssDNA or dsRNA.<ref>PMID:12676087</ref> <ref>PMID:12699629</ref> <ref>PMID:18974281</ref> <ref>PMID:19060897</ref> <ref>PMID:17053788</ref>
+[https://www.uniprot.org/uniprot/EST1A_HUMAN EST1A_HUMAN] Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5'-(GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER).<ref>PMID:12676087</ref> <ref>PMID:12699629</ref> <ref>PMID:18974281</ref> <ref>PMID:19060897</ref> <ref>PMID:17053788</ref>   Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA), but not ssDNA or dsRNA.<ref>PMID:12676087</ref> <ref>PMID:12699629</ref> <ref>PMID:18974281</ref> <ref>PMID:19060897</ref> <ref>PMID:17053788</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 4um2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Serine/threonine protein kinase 3D structures|Serine/threonine protein kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Bonneau, F]]
+[[Category: Bonneau F]]
-[[Category: Chakrabarti, S]]
+[[Category: Chakrabarti S]]
-[[Category: Conti, E]]
+[[Category: Conti E]]
-[[Category: Eppinger, E]]
+[[Category: Eppinger E]]
-[[Category: Schuessler, S]]
+[[Category: Schuessler S]]
-[[Category: Telomerase-binding protein]]
-[[Category: Tpr domain]]

4um2

From Proteopedia

Revision as of 08:28, 22 March 2023

Crystal structure of the TPR domain of SMG6

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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