4tyn: Difference between revisions

Latest revision as of 07:24, 27 September 2023

DEAD-box helicase Mss116 bound to ssDNA and ADP-BeF

Structural highlights

4tyn is a 2 chain structure with sequence from Saccharomyces cerevisiae and 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 2.959Å
Ligands:	ADP, BEF, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MS116_YEAST ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. Here, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.,Mallam AL, Sidote DJ, Lambowitz AM Elife. 2014 Dec 12;3. doi: 10.7554/eLife.04630. PMID:25497230^[5]

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

References

↑ Seraphin B, Simon M, Boulet A, Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature. 1989 Jan 5;337(6202):84-7. PMID:2535893 doi:https://dx.doi.org/10.1038/337084a0
↑ Niemer I, Schmelzer C, Borner GV. Overexpression of DEAD box protein pMSS116 promotes ATP-dependent splicing of a yeast group II intron in vitro. Nucleic Acids Res. 1995 Sep 11;23(17):2966-72. PMID:7567443
↑ Minczuk M, Dmochowska A, Palczewska M, Stepien PP. Overexpressed yeast mitochondrial putative RNA helicase Mss116 partially restores proper mtRNA metabolism in strains lacking the Suv3 mtRNA helicase. Yeast. 2002 Nov;19(15):1285-93. PMID:12402239 doi:https://dx.doi.org/10.1002/yea.906
↑ Huang HR, Rowe CE, Mohr S, Jiang Y, Lambowitz AM, Perlman PS. The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function. Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):163-8. Epub 2004 Dec 23. PMID:15618406 doi:https://dx.doi.org/10.1073/pnas.0407896101
↑ Mallam AL, Sidote DJ, Lambowitz AM. Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. Elife. 2014 Dec 12;3. doi: 10.7554/eLife.04630. PMID:25497230 doi:https://dx.doi.org/10.7554/eLife.04630

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Seraphin B, Simon M, Boulet A, Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature. 1989 Jan 5;337(6202):84-7. PMID:2535893 doi:https://dx.doi.org/10.1038/337084a0

[2] Niemer I, Schmelzer C, Borner GV. Overexpression of DEAD box protein pMSS116 promotes ATP-dependent splicing of a yeast group II intron in vitro. Nucleic Acids Res. 1995 Sep 11;23(17):2966-72. PMID:7567443

[3] Minczuk M, Dmochowska A, Palczewska M, Stepien PP. Overexpressed yeast mitochondrial putative RNA helicase Mss116 partially restores proper mtRNA metabolism in strains lacking the Suv3 mtRNA helicase. Yeast. 2002 Nov;19(15):1285-93. PMID:12402239 doi:https://dx.doi.org/10.1002/yea.906

[4] Huang HR, Rowe CE, Mohr S, Jiang Y, Lambowitz AM, Perlman PS. The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function. Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):163-8. Epub 2004 Dec 23. PMID:15618406 doi:https://dx.doi.org/10.1073/pnas.0407896101

[5] Mallam AL, Sidote DJ, Lambowitz AM. Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. Elife. 2014 Dec 12;3. doi: 10.7554/eLife.04630. PMID:25497230 doi:https://dx.doi.org/10.7554/eLife.04630

[1]

[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='4tyn' size='340' side='right'caption='[[4tyn]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4tyn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TYN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4tyn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [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=4TYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TYN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.959&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4tyw|4tyw]], [[4tyy|4tyy]], [[4tz0|4tz0]], [[4tz6|4tz6]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MSS116, YDR194C, YD9346.05C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tyn OCA], [https://pdbe.org/4tyn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tyn RCSB], [https://www.ebi.ac.uk/pdbsum/4tyn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tyn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST]] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
+[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: RNA helicase]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Lambowitz, A M]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Mallam, A L]]
+[[Category: Lambowitz AM]]
-[[Category: Sidote, D J]]
+[[Category: Mallam AL]]
-[[Category: Dead-box]]
+[[Category: Sidote DJ]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Rna binding protein-dna complex]]
-[[Category: Rna helicase]]

4tyn: Difference between revisions

Latest revision as of 07:24, 27 September 2023

DEAD-box helicase Mss116 bound to ssDNA and ADP-BeF

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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