Induced fit of RNA on binding the L7Ae protein to the kink-turn motif

Turner, Ben; Melcher, Sonya E.; Wilson, Timothy J.; Norman, D.; Lilley, David M.J.

doi:10.1261/rna.2680605

Cited by 101 publications

(117 citation statements)

References 34 publications

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“…Flanking the loop on the 5′ side is a canonical stem with Watson-Crick bps, whereas the 3′ side has two consecutive, sheared GA bps as part of a noncanonical (NC) stem. A sharp kink in the phosphate backbone (the defining feature of this motif) is typically stabilized by proteins and metal ions (32,39) and results in an interaxial angle of ∼60°between the two stems whose nucleotides are now juxtaposed. The diversity of large, cellular RNAs (e.g., rRNA and snoRNAs) that have K-turns attests to this motif's importance in RNA/RNP architecture and function.…”

Section: Resultsmentioning

confidence: 99%

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Cho

Lai

Susanti

et al. 2010

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

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To the mounting evidence of nonribosomal functions for ribosomal proteins, we now add L7Ae as a subunit of archaeal RNase P, a ribonucleoprotein (RNP) that catalyzes 5′-maturation of precursor tRNAs (pre-tRNAs). We first demonstrate that L7Ae coelutes with partially purified Methanococcus maripaludis (Mma) RNase P activity. After establishing in vitro reconstitution of the single RNA with four previously known protein subunits (POP5, RPP21, RPP29, and RPP30), we show that addition of L7Ae to this RNase P complex increases the optimal reaction temperature and k cat ∕K m (by ∼360-fold) for pre-tRNA cleavage to those observed with partially purified native Mma RNase P. We identify in the Mma RNase P RNA a putative kink-turn (K-turn), the structural motif recognized by L7Ae. The large stimulatory effect of Mma L7Ae on RNase P activity decreases to ≤4% of wild type upon mutating either the conserved nucleotides in this K-turn or amino acids in L7Ae shown to be essential for K-turn binding. The critical, multifunctional role of archaeal L7Ae in RNPs acting in tRNA processing (RNase P), RNA modification (H/ACA, C/D snoRNPs), and translation (ribosomes), especially by employing the same RNA-recognition surface, suggests coevolution of various translation-related functions, presumably to facilitate their coordinate regulation.pre-tRNA processing | RPP38 | protein-aided RNA catalysis R Nase P is a Mg 2þ -dependent endoribonuclease that is primarily responsible for catalyzing the removal of the 5′ leaders of precursor-tRNAs (pre-tRNAs) (1-3). Except for some unique organellar variants, RNase P functions in all three domains of life as a ribonucleoprotein (RNP) (1, 2). Although catalysis rests with the essential RNase P RNA (RPR) in all three domains of life (4-6), the RNase P protein (RPP) cofactors play essential roles. In the simple one RPR-one RPP bacterial RNase P, the RPP aids RPR catalysis by enhancing cleavage efficiency and affinity for substrate and Mg 2þ (7-9). The bacterial RPP has not been found in any archaeal or eukaryal genome (10). Eukaryal (nuclear) RNase P, which comprises an RPR and 9 or 10 RPPs (11, 12), has not been reconstituted from recombinant subunits, thus thwarting efforts to uncover the individual functions of eukaryal RPPs. Archaeal RNase P, with an RPR and four RPPs (all homologous to eukaryal RPPs), has therefore been explored as an experimental surrogate for its so-far-intractable eukaryal cousin (13-16). Although native archaeal RNase P has not been characterized, Western analysis and immunoprecipitation validated these four RPPs (POP5, RPP21, RPP29, and RPP30) as being associated with partially purified Methanothermobacter thermautotrophicus (Mth) RNase P activity (14). Subsequent structural and biochemical reconstitution studies using recombinant subunits have proven the utility of archaeal RNase P as a model system to dissect the role of multiple protein cofactors in facilitating RNA catalysis (16).Besides POP5, RPP21, RPP29, and RPP30, weak homologies are evident in the archaeal genomes...

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Section: Resultsmentioning

confidence: 99%

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Cho

Lai

Susanti

et al. 2010

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

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“…32,35,40 To quantitatively identify this motion, principal component analysis (PCA) was carried out on the bound sRNA separately for each trajectory. In general, the three most principal components (named PC1, PC2, and PC3) represent over 80% of the overall fluctuations for ten trajectories.…”

Section: Closing-opening Motion On Two Stems Of Srnamentioning

confidence: 99%

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

Wei¹,

Yang²,

Yu³

et al. 2013

Phys. Chem. Chem. Phys.

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“…The structural principles of K-turns have been analyzed in detail using isostericity matrices by Westhof and colleagues (Lescoute et al 2005). 1 The structure of free K-turn RNA is very dynamic and dependent on the binding of metal ions (Goody et al 2003) or L7Ae-related protein (Turner et al 2005;Wozniak et al 2005). In the absence of protein binding, K-turn RNA exists in an equilibrium between the tightly kinked and a more extended structure, and the position of equilibrium is determined by metal ion concentration.…”

Section: Introductionmentioning

confidence: 99%

The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

Liu

Lilley²

2006

RNA

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137

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The role of 29-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (K-turn) has been investigated. Individual 29-OH groups have been removed by chemical synthesis, and the kinking of the RNA has been studied by gel electrophoresis and fluorescence resonance energy transfer. The results have been analyzed by reference to a database of 11 different crystallographic structures of K-turns. The potential hydrogen bonds fall into several classes. The most important are those in the core of the turn and ribose-phosphate interactions around the bulge. Of these the single most important hydrogen bond is one donated from the 29-OH of the 59 nucleotide of the bulge to the N1 of the adenine of the kink-proximal A d G pair. This is present in all known K-turn structures, and removal of the 29-OH completely prevents metal ion-induced folding. Hydrogen bonds formed in the minor grooves of the helical stems are less important, and removal of the participating 29-OH groups leads to reduced impairment of folding. These interactions are generally more polymorphic, and hydrogen bonds probably form where possible, as permitted by the global structure.

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Induced fit of RNA on binding the L7Ae protein to the kink-turn motif

Cited by 101 publications

References 34 publications

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

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