Structure of the most conserved internal loop in SRP RNA

The signal recognition particle (SRP) directs translating ribosomes to the protein translocation apparatus of endoplasmic reticulum (ER) membrane or the bacterial plasma membrane. The SRP is universally conserved, and in prokaryotes consists of two essential subunits, SRP RNA and SRP54, the latter of which binds to signal sequences on the nascent protein chains. Here we describe the solution NMR structure of a 28-mer RNA composing the most conserved part of SRP RNA to which SRP54 binds. Central to this function is a six-nucleotide internal loop that assumes a novel Mg2+-dependent structure with unusual cross-strand interactions; besides a cross-strand A/A stack, two guanines form hydrogen bonds with opposite-strand phosphates. The structure completely explains the phylogenetic conservation of the loop bases, underlining its importance for SRP54 binding and SRP function.

[1]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197 , 1996 .

[2]  G. Varani,et al.  RNA structure and NMR spectroscopy , 1991, Quarterly Reviews of Biophysics.

[3]  Pascale Legault,et al.  31P chemical shift as a probe of structural motifs in RNA. , 1994, Journal of magnetic resonance. Series B.

[4]  P. Moore,et al.  The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. , 1997, Structure.

[5]  J. A. Newitt,et al.  The E. coli Signal Recognition Particle Is Required for the Insertion of a Subset of Inner Membrane Proteins , 1997, Cell.

[6]  P. Moore,et al.  The sarcin/ricin loop, a modular RNA. , 1995, Journal of molecular biology.

[7]  O. Uhlenbeck,et al.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. , 1987, Nucleic acids research.

[8]  P. Walter,et al.  Human SRP RNA and E. coli 4.5S RNA contain a highly homologous structural domain , 1988, Cell.

[9]  J. Puglisi,et al.  HIV-1 A-rich RNA loop mimics the tRNA anticodon structure , 1998, Nature Structural Biology.

[10]  W. Wintermeyer,et al.  Structure of 4.5S RNA in the signal recognition particle of Escherichia coli as studied by enzymatic and chemical probing. , 1996, RNA.

[11]  T. James,et al.  Correcting NOESY cross-peak intensities for partial relaxation effects enabling accurate distance information. , 1996, Journal of magnetic resonance. Series B.

[12]  L. Gierasch,et al.  Domain interactions in E. coli SRP: stabilization of M domain by RNA is required for effective signal sequence modulation of NG domain. , 1997, Molecular cell.

[13]  H. Heus,et al.  A network of heterogeneous hydrogen bonds in GNRA tetraloops. , 1996, Journal of molecular biology.

[14]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[15]  T. L. James,et al.  Relaxation matrix analysis of 2D NMR data , 1991 .

[16]  T. Powers,et al.  Co‐translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor , 1997, The EMBO journal.

[17]  P. Walter,et al.  Functional substitution of the signal recognition particle 54-kDa subunit by its Escherichia coli homolog. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Smallcombe.  Solvent suppression with symmetrically-shifted pulses , 1993 .

[19]  R. Stroud,et al.  Structure of the conserved GTPase domain of the signal recognition particle , 1997, Nature.

[20]  R. Stroud,et al.  Crystal Structure of the Signal Sequence Binding Subunit of the Signal Recognition Particle , 1998, Cell.

[21]  Evidence for an extended 7SL RNA structure in the signal recognition particle. , 1987, The EMBO journal.

[22]  D E Wemmer,et al.  Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors , 1995, Journal of biomolecular NMR.

[23]  P. Walter,et al.  Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. , 1994, Annual review of cell biology.