The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA

Spitzfaden, Claus; Nicholson, Neville; Jones, Jo J.; Guth, Sabine; Lehr, Ruth; Prescott, Cathy D; Hegg, Lisa A.; Eggleston, Drake S.

doi:10.1006/jmbi.1999.3341

Cited by 98 publications

(102 citation statements)

References 43 publications

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“…These structures reveal that bacterial RNase P proteins share a fold and structure similar to that of the prototypical B. subtilis protein, with an overall abbbaba topology and two RNA binding regions (central cleft and RNR motif) ( Fig. 1; Stams et al 1998;Spitzfaden et al 2000;Kazantsev et al 2003). The central cleft is formed by the central b-sheet and an a-helix (Stams et al 1998).…”

Section: Introductionmentioning

confidence: 83%

“…The structures of several bacterial RNase P proteins have been solved by X-ray crystallography or NMR spectroscopy (Stams et al 1998;Spitzfaden et al 2000;Kazantsev et al 2003). These structures reveal that bacterial RNase P proteins share a fold and structure similar to that of the prototypical B. subtilis protein, with an overall abbbaba topology and two RNA binding regions (central cleft and RNR motif) ( Fig.…”

Section: Introductionmentioning

confidence: 99%

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The RNR motif of B. subtilis RNase P protein interacts with both PRNA and pre-tRNA to stabilize an active conformer

Koutmou¹,

Day-Storms²,

Fierke³

2011

RNA

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Ribonuclease P (RNase P) catalyzes the metal-dependent 59 end maturation of precursor tRNAs (pre-tRNAs). In Bacteria, RNase P is composed of a catalytic RNA (PRNA) and a protein subunit (P protein) necessary for function in vivo. The P protein enhances pre-tRNA affinity, selectivity, and cleavage efficiency, as well as modulates the cation requirement for RNase P function. Bacterial P proteins share little sequence conservation although the protein structures are homologous. Here we combine site-directed mutagenesis, affinity measurements, and single turnover kinetics to demonstrate that two residues (R60 and R62) in the most highly conserved region of the P protein, the RNR motif (R60-R68 in Bacillus subtilis), stabilize PRNA complexes with both P protein (PRNAdP protein) and pre-tRNA (PRNAdP proteindpre-tRNA). Additionally, these data indicate that the RNR motif enhances a metal-stabilized conformational change in RNase P that accompanies substrate binding and is essential for efficient catalysis. Stabilization of this conformational change contributes to both the decreased metal requirement and the enhanced substrate recognition of the RNase P holoenzyme, illuminating the role of the most highly conserved region of P protein in the RNase P reaction pathway.

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Section: Introductionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

The RNR motif of B. subtilis RNase P protein interacts with both PRNA and pre-tRNA to stabilize an active conformer

Koutmou¹,

Day-Storms²,

Fierke³

2011

RNA

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“…Crystal structures have been determined for independently folding ''catalytic'' (C-domain) and ''specificity'' (S-domain) structural domains of the A-and B-types of the bacterial ribozymes (Krasilnikov et al 2003(Krasilnikov et al , 2004Kazantsev et al 2009), for two full-size A-and B-type RNAs (Kazantsev et al 2005;Torres-Larios et al 2005) and, more recently, for the ternary complex between the A-type holoenzyme and the product tRNA (Reiter et al 2010). In addition, crystal structures of bacterial (Stams et al 1998;Spitzfaden et al 2000;Kazantsev et al 2003) and archaeal RNase P protein components (for review, see Evans et al 2006) have been solved, as well as a complex of two eucaryal proteins with a peripheral RNA fragment (Perederina et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Solution structure of RNase P RNA

Kazantsev¹,

Rambo²,

Karimpour³

et al. 2011

RNA

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The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 29-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity.

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“…Structural studies of RNase P proteins have so far been limited to B-type proteins, from the low GϩC Gram-positive bacteria Bacillus subtilis (17) and Staphylococcus aureus (18). These proteins have a high degree of similarity, but are closely related and so do not provide much comparative perspective.…”

mentioning

confidence: 99%

High-resolution structure of RNase P protein from Thermotoga maritima

Kazantsev

Krivenko

Harrington

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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The structure of RNase P protein from the hyperthermophilic bacterium Thermotoga maritima was determined at 1.2-Å resolution by using x-ray crystallography. This protein structure is from an ancestral-type RNase P and bears remarkable similarity to the recently determined structures of RNase P proteins from bacteria that have the distinct, Bacillus type of RNase P. These two types of protein span the extent of bacterial RNase P diversity, so the results generalize the structure of the bacterial RNase P protein. The broad phylogenetic conservation of structure and distribution of potential RNA-binding elements in the RNase P proteins indicate that all of these homologous proteins bind to their cognate RNAs primarily by interaction with the phylogenetically conserved core of the RNA. The protein is found to dimerize through an extensive, well-ordered interface. This dimerization may reflect a mechanism of thermal stability of the protein before assembly with the RNA moiety of the holoenzyme. RNase P catalyzes the divalent metal-dependent hydrolysis of a specific phosphodiester bond in pre-tRNAs, to release the 5Ј precursor sequences and produce the mature 5Ј ends of the tRNAs (see refs. 1-4 for reviews). All RNase P species studied to date are complex holoenzymes composed of one RNA and at least one protein component. The bacterial RNase P typically consists of a large RNA (350-400 nt; 100-130 kDa) and one small (Ϸ120 aa; 12-13 kDa) protein subunit. The active site of the bacterial RNase P is contained within the RNA. This is shown by the catalytic activity of the RNA in the absence of the protein moiety in vitro, at high ionic strength (5). At physiological ionic strength and in vivo, however, the protein component is required for pre-tRNA processing (5, 6).The role of the bacterial RNase P protein in the RNase P reaction is not entirely clear. The fact that it confers high activity on the RNA at physiological ionic strength suggests that the protein stabilizes the holoenzyme against electrostatic distortion (7). In vitro, the protein component of bacterial RNase P has been implicated in increasing the turnover rate of the enzyme (7), possibly by contribution to specific binding of the substrate over the product (8). Some mutational, enzymatic, and photoaffinity crosslinking studies have been interpreted to indicate that in the bacterial holoenzyme RNase P protein may form direct contacts with the 5Ј precursor sequence of the substrate pretRNA (9-11). The structural basis of any such interaction is not known. Moreover, there is no consistent structural model for the interaction between the protein and the RNase P RNA, despite several crosslink and footprint studies (11)(12)(13)(14).Phylogenetic comparative analysis has identified two major structural types of bacterial RNase P RNA (15). Both types have a homologous core structure that consists of about half the sequence lengths of the RNAs, but about half the sequence of each type of RNA has no homologous counterpart in the other RNA. The ancestral type (A type) ...

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The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA

Cited by 98 publications

References 43 publications

The RNR motif of B. subtilis RNase P protein interacts with both PRNA and pre-tRNA to stabilize an active conformer

The RNR motif of B. subtilis RNase P protein interacts with both PRNA and pre-tRNA to stabilize an active conformer

Solution structure of RNase P RNA

High-resolution structure of RNase P protein from Thermotoga maritima

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