5fg1

From Proteopedia

(Difference between revisions)

Current revision

Structure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal domain, TRIGONAL FORM

Structural highlights

5fg1 is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.55Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LTN1_YEAST E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23178123). Mediates ubiquitination of proteins derived from mRNAs lacking stop codons (non-stop proteins) and other translation arrest products induced by poly-lysine sequences and tandem rare codons. Ubiquitination leads to CDC48 recruitment for extraction and degradation of the incomplete translation product (PubMed:20835226, PubMed:23825054, PubMed:24261871). May indirectly play a role in chromatin function and transcription (PubMed:17283062).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The Ltn1 E3 ligase (listerin in mammals) has emerged as a paradigm for understanding ribosome-associated ubiquitylation. Ltn1 binds to 60S ribosomal subunits to ubiquitylate nascent polypeptides that become stalled during synthesis; among Ltn1's substrates are aberrant products of mRNA lacking stop codons [nonstop translation products (NSPs)]. Here, we report the reconstitution of NSP ubiquitylation in Neurospora crassa cell extracts. Upon translation in vitro, ribosome-stalled NSPs were ubiquitylated in an Ltn1-dependent manner, while still ribosome-associated. Furthermore, we provide biochemical evidence that the conserved N-terminal domain (NTD) plays a significant role in the binding of Ltn1 to 60S ribosomal subunits and that NTD mutations causing defective 60S binding also lead to defective NSP ubiquitylation, without affecting Ltn1's intrinsic E3 ligase activity. Finally, we report the crystal structure of the Ltn1 NTD at 2.4-A resolution. The structure, combined with additional mutational studies, provides insight to NTD's role in binding stalled 60S subunits. Our findings show that Neurospora extracts can be used as a tool to dissect mechanisms underlying ribosome-associated protein quality control and are consistent with a model in which Ltn1 uses 60S subunits as adapters, at least in part via its NTD, to target stalled NSPs for ubiquitylation.

Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits.,Doamekpor SK, Lee JW, Hepowit NL, Wu C, Charenton C, Leonard M, Bengtson MH, Rajashankar KR, Sachs MS, Lima CD, Joazeiro CA Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4151-60. doi:, 10.1073/pnas.1605951113. Epub 2016 Jul 6. PMID:27385828^[6]

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

References

↑ Braun MA, Costa PJ, Crisucci EM, Arndt KM. Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol Cell Biol. 2007 Apr;27(8):2800-11. Epub 2007 Feb 5. PMID:17283062 doi:http://dx.doi.org/10.1128/MCB.01947-06
↑ Bengtson MH, Joazeiro CA. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. Nature. 2010 Sep 23;467(7314):470-3. doi: 10.1038/nature09371. Epub 2010 Sep 12. PMID:20835226 doi:http://dx.doi.org/10.1038/nature09371
↑ Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell. 2012 Nov 21;151(5):1042-54. doi: 10.1016/j.cell.2012.10.044. PMID:23178123 doi:http://dx.doi.org/10.1016/j.cell.2012.10.044
↑ Letzring DP, Wolf AS, Brule CE, Grayhack EJ. Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1. RNA. 2013 Sep;19(9):1208-17. doi: 10.1261/rna.039446.113. Epub 2013 Jul 3. PMID:23825054 doi:http://dx.doi.org/10.1261/rna.039446.113
↑ Matsuda R, Ikeuchi K, Nomura S, Inada T. Protein quality control systems associated with no-go and nonstop mRNA surveillance in yeast. Genes Cells. 2014 Jan;19(1):1-12. doi: 10.1111/gtc.12106. Epub 2013 Nov 21. PMID:24261871 doi:http://dx.doi.org/10.1111/gtc.12106
↑ Doamekpor SK, Lee JW, Hepowit NL, Wu C, Charenton C, Leonard M, Bengtson MH, Rajashankar KR, Sachs MS, Lima CD, Joazeiro CA. Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits. Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4151-60. doi:, 10.1073/pnas.1605951113. Epub 2016 Jul 6. PMID:27385828 doi:http://dx.doi.org/10.1073/pnas.1605951113

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/5fg1"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Doamekpor SK | Lima CD

@@ Line 1: / Line 1: @@
 ==Structure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal domain, TRIGONAL FORM==
-<StructureSection load='5fg1' size='340' side='right' caption='[[5fg1]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='5fg1' size='340' side='right'caption='[[5fg1]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5fg1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FG1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FG1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5fg1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FG1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FG1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.55&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fg0|5fg0]]</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=5fg1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fg1 OCA], [https://pdbe.org/5fg1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fg1 RCSB], [https://www.ebi.ac.uk/pdbsum/5fg1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fg1 ProSAT]</span></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=5fg1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fg1 OCA], [http://pdbe.org/5fg1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fg1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fg1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fg1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LTN1_YEAST LTN1_YEAST]] E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23178123). Mediates ubiquitination of proteins derived from mRNAs lacking stop codons (non-stop proteins) and other translation arrest products induced by poly-lysine sequences and tandem rare codons. Ubiquitination leads to CDC48 recruitment for extraction and degradation of the incomplete translation product (PubMed:20835226, PubMed:23825054, PubMed:24261871). May indirectly play a role in chromatin function and transcription (PubMed:17283062).<ref>PMID:17283062</ref> <ref>PMID:20835226</ref> <ref>PMID:23178123</ref> <ref>PMID:23825054</ref> <ref>PMID:24261871</ref>
+[https://www.uniprot.org/uniprot/LTN1_YEAST LTN1_YEAST] E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23178123). Mediates ubiquitination of proteins derived from mRNAs lacking stop codons (non-stop proteins) and other translation arrest products induced by poly-lysine sequences and tandem rare codons. Ubiquitination leads to CDC48 recruitment for extraction and degradation of the incomplete translation product (PubMed:20835226, PubMed:23825054, PubMed:24261871). May indirectly play a role in chromatin function and transcription (PubMed:17283062).<ref>PMID:17283062</ref> <ref>PMID:20835226</ref> <ref>PMID:23178123</ref> <ref>PMID:23825054</ref> <ref>PMID:24261871</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 5fg1" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Doamekpor, S K]]
+[[Category: Large Structures]]
-[[Category: Lima, C D]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Ligase]]
+[[Category: Doamekpor SK]]
-[[Category: Protein quality control]]
+[[Category: Lima CD]]
-[[Category: Ribosome]]
-[[Category: Ubiquitin ligase]]

5fg1

From Proteopedia

Current revision

Structure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal domain, TRIGONAL FORM

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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