6ah3

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Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate

Structural highlights

6ah3 is a 12 chain structure with sequence from [1], Baker's yeast and Saccharomyces cerevisiae (strain atcc 204508 / s288c). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:Ribonuclease P, with EC number 3.1.26.5
Experimental data:Check to display Experimental Data
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POP6_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP, which cleaves pre-rRNA sequences.[1] [POP3_YEAST] Required for processing of 5.8S rRNA (short form) at site A3 and for 5'- and 3'-processing of pre-tRNA.[2] [3] [POP7_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP, which cleaves pre-rRNA sequences.[4] [5] [RPP1_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP, which cleaves pre-rRNA sequences.[6] [7] [POP1_YEAST] Required for processing of 5.8S rRNA (short form) at site A3 and for 5' and 3' processing of pre-tRNA.[8] [9] [POP8_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP, which cleaves pre-rRNA sequences.[10] [POP4_YEAST] Required for 5.8S rRNA and tRNA processing; associated with RNase MRP and RNase P.[11] [12] [RPR2_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[13] [POP5_YEAST] Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP, which cleaves pre-rRNA sequences.[14]

Publication Abstract from PubMed

Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-tRNA. Here we report the 3.5-A cryo-EM structures of Saccharomyces cerevisiae RNase P alone and in complex with pre-tRNA(Phe) The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a "measuring device" with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3' leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion SN2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5'-leader of pre-tRNA is processed by eukaryotic RNase P.

Structural insight into precursor tRNA processing by yeast ribonuclease P.,Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M Science. 2018 Sep 27. pii: science.aat6678. doi: 10.1126/science.aat6678. PMID:30262633[15]

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

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See Also

References

  1. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  2. ↑ Dichtl B, Tollervey D. Pop3p is essential for the activity of the RNase MRP and RNase P ribonucleoproteins in vivo. EMBO J. 1997 Jan 15;16(2):417-29. PMID:9029160
  3. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  4. ↑ Stolc V, Katz A, Altman S. Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6716-21. PMID:9618478
  5. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  6. ↑ Stolc V, Altman S. Rpp1, an essential protein subunit of nuclear RNase P required for processing of precursor tRNA and 35S precursor rRNA in Saccharomyces cerevisiae. Genes Dev. 1997 Sep 15;11(18):2414-25. PMID:9308968
  7. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  8. ↑ Lygerou Z, Mitchell P, Petfalski E, Seraphin B, Tollervey D. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev. 1994 Jun 15;8(12):1423-33. PMID:7926742
  9. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  10. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  11. ↑ Chu S, Zengel JM, Lindahl L. A novel protein shared by RNase MRP and RNase P. RNA. 1997 Apr;3(4):382-91. PMID:9085845
  12. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  13. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  14. ↑ Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 1998 Jun 1;12(11):1678-90. PMID:9620854
  15. ↑ Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M. Structural insight into precursor tRNA processing by yeast ribonuclease P. Science. 2018 Sep 27. pii: science.aat6678. doi: 10.1126/science.aat6678. PMID:30262633 doi:http://dx.doi.org/10.1126/science.aat6678

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6ah3, resolution 3.48Å

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