Solution Structure of Prokaryotic Ribosomal Protein S17 by High-Resolution NMR Spectroscopy

Jaishree, T.N.; Ramakrishnan, V.; White, Stephen W.

doi:10.1021/bi951062i

Cited by 43 publications

(29 citation statements)

References 68 publications

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“…It has been suggested that as ancient proteins, ribosomal proteins might define families of protein folds, which are also used in other protein–RNA interactions (Bycroft et al ., 1997). The family represented by Asp‐/Phe‐/Lys‐tRNA synthetases (Cavarelli et al ., 1993; Mosyak et al ., 1995; Onesti et al ., 1995), the cold shock domain proteins (Newkirk et al ., 1994; Schindelin et al ., 1994) and the ribosomal proteins S1 and S17 (Jaishree et al ., 1996; Bycroft et al ., 1997) seems to be one good example. Sequence homologues of L25 include CTC stress proteins (Gryaznova et al ., 1996) and the topology of the β‐barrel of L25 has so far only been observed in glutaminyl‐tRNA‐synthetases (GlnRS; Rould et al ., 1991; Stoldt et al ., 1998), albeit in the latter case with very little sequence homology to L25.…”

Section: Discussionmentioning

confidence: 99%

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

Stoldt

Wöhnert

Ohlenschläger

et al. 1999

EMBO J

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M.Stoldt and J.Wöhnert contributed equally to this workThe structure of the complex between ribosomal protein L25 and a 37 nucleotide RNA molecule, which contains the E-loop and helix IV regions of the E-domain of Escherichia coli 5S rRNA, has been determined to an overall r.m.s. displacement of 1.08 Å (backbone heavy atoms) by heteronuclear NMR spectroscopy (Protein Databank code 1d6k). The interacting molecular surfaces are bipartite for both the RNA and the protein. One side of the six-stranded β-barrel of L25 recognizes the minor groove of the E-loop with very little change in the conformations of either the protein or the RNA and with the RNA-protein interactions occurring mainly along one strand of the E-loop duplex. This minor groove recognition module includes two parallel β-strands of L25, a hitherto unknown RNA binding topology. Binding of the RNA also induces conversion of a flexible loop to an α-helix in L25, the N-terminal tip of which interacts with the widened major groove at the E-loop/helix IV junction of the RNA. The structure of the complex reveals that the E-domain RNA serves as a preformed docking partner, while the L25 protein has one preformed and one induced recognition module.

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Section: Discussionmentioning

confidence: 99%

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

Stoldt

Wöhnert

Ohlenschläger

et al. 1999

EMBO J

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“…In addition to protein L9, the structures of L7/L12 (Leijonmarck et al, 1980), L30 (Wilson et al, 1986), S5 (Ramakrishnan & White, 1992), L6 (Golden et al, 1994), S17 (Golden et al, 1993;Jaishree et al, 1996) and S6 (Lindahl et al, 1994), L14 (Davies et al, 1996a), L1 (Nikonov et al, 1996) and S8 (Davies et al, 1996b) have been reported. NMR methods have also been used to study the structures of several ribosomal RNA fragments (Varani et al, 1991;Heus & Pardi, 1991;Szewczak et al, 1993;Dallas et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Ribosomal Protein L9: A Structure Determination by the Combined Use of X-ray Crystallography and NMR Spectroscopy

Hoffman

Cameron

Davies

et al. 1996

Journal of Molecular Biology

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“…Protein S17 binds helices 7 and 11 near the central junction 10. Its flexible loops extend from a β-barrel 11 to contact different regions of the rRNA. Amino acids 13-17 in S17 stabilize a K-turn in helix 11, while aa 29-34 thread between helix 11 and helix 21 to reach the 560-region at the junction with the central domain 12.…”

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confidence: 99%

Global Stabilization of rRNA Structure by Ribosomal Proteins S4, S17, and S20

Ramaswamy

Woodson

2009

Journal of Molecular Biology

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SummaryRibosomal proteins stabilize the folded structure of the rRNA and enable the recruitment of further proteins to the complex. Quantitative hydroxyl radical footprinting was used to measure the extent to which three different primary assembly proteins, S4, S17 and S20, stabilize the 3D structure of the E. coli 16S 5′ domain. The stability of the complexes was perturbed by varying the concentration of MgCl 2 . Each protein influences the stability of the rRNA tertiary interactions beyond its immediate binding site. S4 and S17 stabilize the entire 5′ domain, while S20 has a more local effect. Multi-stage folding of individual helices within the 5′ domain shows that each protein stabilizes a different ensemble of structural intermediates, that include non-native interactions at low Mg 2+ . We propose that the combined interactions of S4, S17 and S20 with different helical junctions bias the free energy landscape toward a few RNA conformations that are competent to add the secondary assembly protein S16 in the next step of assembly. Keywordsribosome; ribosomal protein; RNA folding; hydroxyl radical footprinting; RNA-protein interactions Ribosome biogenesis is one of the most important synthetic tasks undertaken by the cell. Among bacteria, short generation times require that several hundreds of ribosomes are produced per minute in order to produce the tens of thousands of ribosomes needed by each new cell 1;2 . A critical question is how the RNA and protein components of the ribosome interact to achieve the native subunits and avoid nonfunctional complexes.Studies on the reconstitution of the 30S ribosomal subunit have shown that binding of ribosomal proteins is coupled to folding of the rRNA 3;4 . The addition of the primary assembly proteins, which bind directly to the 16S rRNA, stabilize the helices with which they interact, and enable further assembly of each 30S domain by pre-ordering the binding sites for secondary and tertiary assembly proteins 5;6 . The extent to which individual ribosomal proteins stabilize the structure of the rRNA beyond their immediate binding site is thus directly connected to the hierarchy and cooperativity of assembly 4;7 .

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Solution Structure of Prokaryotic Ribosomal Protein S17 by High-Resolution NMR Spectroscopy

Cited by 43 publications

References 68 publications

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

Ribosomal Protein L9: A Structure Determination by the Combined Use of X-ray Crystallography and NMR Spectroscopy

Global Stabilization of rRNA Structure by Ribosomal Proteins S4, S17, and S20

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