2xzl: Difference between revisions

Revision as of 10:42, 20 December 2023

Upf1-RNA complex

Structural highlights

2xzl is a 2 chain structure with sequence from Saccharomyces cerevisiae and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	1PE, ADP, ALF, MG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RENT1_YEAST RNA-dependent helicase required for nonsense-mediated decay (NMD) of aberrant mRNAs containing premature stop codons and modulates the expression level of normal mRNAs (PubMed:8896465, PubMed:30218034). Also capable of unwinding double-stranded DNA and translocating on single-stranded DNA (PubMed:30218034).^[1] ^[2]

Publication Abstract from PubMed

Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3. We report crystal structures of Upf1 in the presence and absence of the CH domain, captured in the transition state with ADP:AlF(4)(-) and RNA. In isolation, Upf1 clamps onto the RNA, enclosing it in a channel formed by both the catalytic and regulatory domains. Upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. Formation of the surveillance complex thus modifies the RNA binding properties and the catalytic activity of Upf1, causing it to switch from an RNA-clamping mode to an RNA-unwinding mode.

Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2.,Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E Mol Cell. 2011 Mar 18;41(6):693-703. PMID:21419344^[3]

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

References

↑ Kanaan J, Raj S, Decourty L, Saveanu C, Croquette V, Le Hir H. UPF1-like helicase grip on nucleic acids dictates processivity. Nat Commun. 2018 Sep 14;9(1):3752. PMID:30218034 doi:10.1038/s41467-018-06313-y
↑ Cui Y, Dinman JD, Peltz SW. Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. EMBO J. 1996 Oct 15;15(20):5726-36. PMID:8896465 doi:10.1002/j.1460-2075.1996.tb00956.x
↑ Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E. Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2. Mol Cell. 2011 Mar 18;41(6):693-703. PMID:21419344 doi:10.1016/j.molcel.2011.02.010

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OCA

[1] Kanaan J, Raj S, Decourty L, Saveanu C, Croquette V, Le Hir H. UPF1-like helicase grip on nucleic acids dictates processivity. Nat Commun. 2018 Sep 14;9(1):3752. PMID:30218034 doi:10.1038/s41467-018-06313-y

[2] Cui Y, Dinman JD, Peltz SW. Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. EMBO J. 1996 Oct 15;15(20):5726-36. PMID:8896465 doi:10.1002/j.1460-2075.1996.tb00956.x

[3] Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E. Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2. Mol Cell. 2011 Mar 18;41(6):693-703. PMID:21419344 doi:10.1016/j.molcel.2011.02.010

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2xzl' size='340' side='right'caption='[[2xzl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xzl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xzl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2xzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzl OCA], [https://pdbe.org/2xzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xzl RCSB], [https://www.ebi.ac.uk/pdbsum/2xzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NAM7_YEAST NAM7_YEAST]] Probable helicase involved in mitochondrial functions. Required for rapid turnover of mRNAs containing a premature translational termination codon.
+[https://www.uniprot.org/uniprot/RENT1_YEAST RENT1_YEAST] RNA-dependent helicase required for nonsense-mediated decay (NMD) of aberrant mRNAs containing premature stop codons and modulates the expression level of normal mRNAs (PubMed:8896465, PubMed:30218034). Also capable of unwinding double-stranded DNA and translocating on single-stranded DNA (PubMed:30218034).<ref>PMID:30218034</ref> <ref>PMID:8896465</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: RNA helicase]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Basquin, C]]
+[[Category: Synthetic construct]]
-[[Category: Bonneau, F]]
+[[Category: Basquin C]]
-[[Category: Chakrabarti, S]]
+[[Category: Bonneau F]]
-[[Category: Conti, E]]
+[[Category: Chakrabarti S]]
-[[Category: Domcke, S]]
+[[Category: Conti E]]
-[[Category: Fiorini, F]]
+[[Category: Domcke S]]
-[[Category: Hir, H Le]]
+[[Category: Fiorini F]]
-[[Category: Jayachandran, U]]
+[[Category: Jayachandran U]]
-[[Category: Allosteric regulation]]
+[[Category: Le Hir H]]
-[[Category: Hydrolase-rna complex]]
-[[Category: Nmd]]
-[[Category: Rna degradation]]

2xzl: Difference between revisions

Revision as of 10:42, 20 December 2023

Upf1-RNA complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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