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PDBsum entry 1k6h
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RNA PDB id
1k6h

 

 

 

 

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Contents
DNA/RNA
PDB id:
1k6h
Name: RNA
Title: Solution structure of conserved agnn tetraloops: insights into rnt1p RNA processing
Structure: RNA (5'- r(p Gp Gp Cp Gp Up Gp Up Up Cp Ap Gp Ap Ap Gp Ap Ap Cp Gp Cp Gp Cp C) -3'). Chain: a. Engineered: yes. Other_details: agnn tetraloop, substrate for rnt1p
Source: Synthetic: yes. Other_details: synthetic-t7 RNA transcript
NMR struc: 20 models
Authors: I.Lebars,B.Lamontagne,S.Yoshizawa,S.Abou Elela,D.Fourmy
Key ref:
I.Lebars et al. (2001). Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing. EMBO J, 20, 7250-7258. PubMed id: 11743001 DOI: 10.1093/emboj/20.24.7250
Date:
16-Oct-01     Release date:   19-Dec-01    
 Headers
 References

DNA/RNA chain
  G-G-C-G-U-G-U-U-C-A-G-A-A-G-A-A-C-G-C-G-C-C 22 bases

 

 
DOI no: 10.1093/emboj/20.24.7250 EMBO J 20:7250-7258 (2001)
PubMed id: 11743001  
 
 
Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing.
I.Lebars, B.Lamontagne, S.Yoshizawa, S.Aboul-Elela, D.Fourmy.
 
  ABSTRACT  
 
Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A-A or A-C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5' side of the loop, exposing their Watson-Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Illustration of Rnt1p model substrates. The conserved AGNN nucleotides are shown in bold. The mutations introduced in the wild-type sequence are shown in grey. The four heterologous base pairs used to stabilize the structure are shown as an outline. R31 represents the terminal stem -loop of the U5 snRNA. R32 represents the terminal stem -loop of snR47. R31U is R31 with a mutation that changes the conserved A residue in the tetraloop to U. R31A contains the R31 stem sequence but the loop sequence is changed to GAAA. R31L contains the R31 sequence and an insertion of 10 bp that extends the stem size to a total of 19 bp. The sites of cleavages by Rnt1p are indicated by the arrowheads. 		Figure 6.
Figure 6 Stereo views of single representative structures of AGUC (A) and AGAA (B) tetraloops. All heavy atoms are displayed. Bases are coloured in light blue, with nitrogen and oxygen atoms in dark blue and red, respectively. Ribose -phosphate backbones are coloured in yellow, and phosphate oxygen in red.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 7250-7258) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17534422 B.Lamontagne, and S.Abou Elela (2007).
Short RNA guides cleavage by eukaryotic RNase III.
  PLoS ONE, 2, e472.  
17158880 S.Larose, N.Laterreur, G.Ghazal, J.Gagnon, R.J.Wellinger, and S.A.Elela (2007).
RNase III-dependent regulation of yeast telomerase.
  J Biol Chem, 282, 4373-4381.  
15798187 G.Ghazal, D.Ge, J.Gervais-Bird, J.Gagnon, and S.Abou Elela (2005).
Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals.
  Mol Cell Biol, 25, 2981-2994.  
15840813 R.Stefl, and F.H.Allain (2005).
A novel RNA pentaloop fold involved in targeting ADAR2.
  RNA, 11, 592-597.
PDB code: 1ysv
15687383 T.Sakamoto, A.Oguro, G.Kawai, T.Ohtsu, and Y.Nakamura (2005).
NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A.
  Nucleic Acids Res, 33, 745-754.
PDB codes: 1xwp 1xwu
15525710 A.W.Faber, J.C.Vos, H.R.Vos, G.Ghazal, S.A.Elela, and H.A.Raué (2004).
The RNA catabolic enzymes Rex4p, Rnt1p, and Dbr1p show genetic interaction with trans-acting factors involved in processing of ITS1 in Saccharomyces cerevisiae pre-rRNA.
  RNA, 10, 1946-1956.  
14581474 B.Lamontagne, and S.A.Elela (2004).
Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage.
  J Biol Chem, 279, 2231-2241.  
15150409 H.Wu, A.Henras, G.Chanfreau, and J.Feigon (2004).
Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III.
  Proc Natl Acad Sci U S A, 101, 8307-8312.
PDB code: 1t4l
15192703 N.Leulliot, S.Quevillon-Cheruel, M.Graille, H.van Tilbeurgh, T.C.Leeper, K.S.Godin, T.E.Edwards, S.T.Sigurdsson, N.Rozenkrants, R.J.Nagel, M.Ares, and G.Varani (2004).
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.
  EMBO J, 23, 2468-2477.
PDB codes: 1t4n 1t4o
12888491 D.W.Staple, and S.E.Butcher (2003).
Solution structure of the HIV-1 frameshift inducing stem-loop RNA.
  Nucleic Acids Res, 31, 4326-4331.
PDB code: 1pjy
12736295 S.H.Chou, K.H.Chin, and A.H.Wang (2003).
Unusual DNA duplex and hairpin motifs.
  Nucleic Acids Res, 31, 2461-2474.  
12734190 T.J.Bollenbach, and D.B.Stern (2003).
Secondary structures common to chloroplast mRNA 3'-untranslated regions direct cleavage by CSP41, an endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.
  J Biol Chem, 278, 25832-25838.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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