7a9w

Structure of yeast Rmd9p in complex with 20nt target RNAStructure of yeast Rmd9p in complex with 20nt target RNA

Structural highlights

7a9w 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 2.55Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RMD9_YEAST Binds the RNA motif 5'-AAUAA[U/C]AUUCUU-3' in the 3'-UTR of mitochondrial mRNAs (PubMed:10441495, PubMed:10905425, PubMed:33876744). Involved in the processing or stability of mitochondrial mRNAs (PubMed:17194786, PubMed:17194787, PubMed:33876744).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5' capping and 3' polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3'-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3'-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs.,Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. doi: , 10.1073/pnas.2009329118. PMID:33876744^[6]

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

References

↑ Li H, Zassenhaus HP. Purification and characterization of an RNA dodecamer sequence binding protein from mitochondria of Saccharomyces cerevisiae. Biochem Biophys Res Commun. 1999 Aug 11;261(3):740-5. PMID:10441495 doi:10.1006/bbrc.1999.1085
↑ Li H, Zassenhaus HP. Phosphorylation is required for high-affinity binding of DBP, a yeast mitochondrial site-specific RNA binding protein. Curr Genet. 2000 Jun;37(6):356-63. PMID:10905425 doi:10.1007/s002940000117
↑ Williams EH, Butler CA, Bonnefoy N, Fox TD. Translation initiation in Saccharomyces cerevisiae mitochondria: functional interactions among mitochondrial ribosomal protein Rsm28p, initiation factor 2, methionyl-tRNA-formyltransferase and novel protein Rmd9p. Genetics. 2007 Mar;175(3):1117-26. PMID:17194786 doi:10.1534/genetics.106.064576
↑ Nouet C, Bourens M, Hlavacek O, Marsy S, Lemaire C, Dujardin G. Rmd9p controls the processing/stability of mitochondrial mRNAs and its overexpression compensates for a partial deficiency of oxa1p in Saccharomyces cerevisiae. Genetics. 2007 Mar;175(3):1105-15. PMID:17194787 doi:10.1534/genetics.106.063883
↑ Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. PMID:33876744 doi:10.1073/pnas.2009329118
↑ Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. PMID:33876744 doi:10.1073/pnas.2009329118

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OCA

[1] Li H, Zassenhaus HP. Purification and characterization of an RNA dodecamer sequence binding protein from mitochondria of Saccharomyces cerevisiae. Biochem Biophys Res Commun. 1999 Aug 11;261(3):740-5. PMID:10441495 doi:10.1006/bbrc.1999.1085

[2] Li H, Zassenhaus HP. Phosphorylation is required for high-affinity binding of DBP, a yeast mitochondrial site-specific RNA binding protein. Curr Genet. 2000 Jun;37(6):356-63. PMID:10905425 doi:10.1007/s002940000117

[3] Williams EH, Butler CA, Bonnefoy N, Fox TD. Translation initiation in Saccharomyces cerevisiae mitochondria: functional interactions among mitochondrial ribosomal protein Rsm28p, initiation factor 2, methionyl-tRNA-formyltransferase and novel protein Rmd9p. Genetics. 2007 Mar;175(3):1117-26. PMID:17194786 doi:10.1534/genetics.106.064576

[4] Nouet C, Bourens M, Hlavacek O, Marsy S, Lemaire C, Dujardin G. Rmd9p controls the processing/stability of mitochondrial mRNAs and its overexpression compensates for a partial deficiency of oxa1p in Saccharomyces cerevisiae. Genetics. 2007 Mar;175(3):1105-15. PMID:17194787 doi:10.1534/genetics.106.063883

[5] Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. PMID:33876744 doi:10.1073/pnas.2009329118

[6] Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2009329118. PMID:33876744 doi:10.1073/pnas.2009329118

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