This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4db4

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 17:08, 24 December 2014

Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex

Structural highlights

4db4 is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	4dax, 4daz, 4db2
Gene:	MSS116, YDR194C, YD9346.05C (Saccharomyces cerevisiae)
Activity:	RNA helicase, with EC number 3.6.4.13
Resources:	FirstGlance, OCA, RCSB, PDBsum

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

DEAD-box proteins are the largest family of nucleic acid helicases, and are crucial to RNA metabolism throughout all domains of life. They contain a conserved 'helicase core' of two RecA-like domains (domains (D)1 and D2), which uses ATP to catalyse the unwinding of short RNA duplexes by non-processive, local strand separation. This mode of action differs from that of translocating helicases and allows DEAD-box proteins to remodel large RNAs and RNA-protein complexes without globally disrupting RNA structure. However, the structural basis for this distinctive mode of RNA unwinding remains unclear. Here, structural, biochemical and genetic analyses of the yeast DEAD-box protein Mss116p indicate that the helicase core domains have modular functions that enable a novel mechanism for RNA-duplex recognition and unwinding. By investigating D1 and D2 individually and together, we find that D1 acts as an ATP-binding domain and D2 functions as an RNA-duplex recognition domain. D2 contains a nucleic-acid-binding pocket that is formed by conserved DEAD-box protein sequence motifs and accommodates A-form but not B-form duplexes, providing a basis for RNA substrate specificity. Upon a conformational change in which the two core domains join to form a 'closed state' with an ATPase active site, conserved motifs in D1 promote the unwinding of duplex substrates bound to D2 by excluding one RNA strand and bending the other. Our results provide a comprehensive structural model for how DEAD-box proteins recognize and unwind RNA duplexes. This model explains key features of DEAD-box protein function and affords a new perspective on how the evolutionarily related cores of other RNA and DNA helicases diverged to use different mechanisms.

Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p.,Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM Nature. 2012 Sep 2. doi: 10.1038/nature11402. PMID:22940866^[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:http://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:http://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:http://dx.doi.org/10.1073/pnas.0407896101
↑ Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM. Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p. Nature. 2012 Sep 2. doi: 10.1038/nature11402. PMID:22940866 doi:http://dx.doi.org/10.1038/nature11402

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4db4"

@@ Line 8: / Line 8: @@
 <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=4db4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4db4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4db4 RCSB], [http://www.ebi.ac.uk/pdbsum/4db4 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://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 ==

4db4

From Proteopedia

Revision as of 17:08, 24 December 2014

Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox