5S rRNA sugar‐phosphate backbone protection in complexes with specific ribosomal proteins

Shpanchenko, Olga V.; Zvereva, Maria I.; Dontsova, Olga А.; Nierhaus, Knud H.; Bøgdanov, A.

doi:10.1016/0014-5793(96)00872-1

Cited by 15 publications

(8 citation statements)

References 18 publications

(25 reference statements)

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“…Reconstituted 50S ribosomal subunits lacking the 5S rRNA are inactive in protein biosynthesis (Erdmann et al ., 1971; Hartmann et al ., 1988). The distal end of the E‐domain (also referred to as domain IV) of the 5S rRNA, which is directly adjacent to the E‐loop binding site for the L25 protein (Douthwaite et al ., 1979; Garrett and Noller, 1979; Huber and Wool, 1984; Ciesiolka et al ., 1992; Shpanchenko et al ., 1996), has been shown to reside in proximity to the peptidyl transferase ring and the GTPase‐associated area of the 23S rRNA leading to the suggestion that this domain might play an as yet unidentified role in the process of peptide bond formation (Dontsova et al ., 1994; Sergiev et al ., 1998).…”

Section: Introductionmentioning

confidence: 99%

The NMR structure ofEscherichia coliribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases

et al. 1998

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Section: Introductionmentioning

confidence: 99%

The NMR structure ofEscherichia coliribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases

et al. 1998

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“…Further, the major groove of ''helix IV,'' which lies adjacent to loop E is likewise significantly widened, implying its potential accessibility to sequence-specific protein interactions. Biochemical protection, modification, and interference studies imply that L25 binds to the portion of 5S rRNA including the minor groove side of loop E and the adjacent major groove of helix IV (3)(4)(5)(6)(7).…”

mentioning

confidence: 99%

Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-Å resolution

Steitz

2000

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

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The crystal structure of Escherichia coli ribosomal protein L25 bound to an 18-base pair portion of 5S ribosomal RNA, which contains ''loop E,'' has been determined at 1.8-Å resolution. The protein primarily recognizes a unique RNA shape, although five side chains make direct or water-mediated interactions with bases. Three ␤-strands lie in the widened minor groove of loop E formed by noncanonical base pairs and cross-strand purine stacks, and an ␣-helix interacts in an adjacent widened major groove. The structure of loop E is largely the same as that of uncomplexed RNA (rms deviation of 0.4 Å for 11 base pairs), and 3 Mg 2؉ ions that stabilize the noncanonical base pairs lie in the same or similar locations in both structures. Perhaps surprisingly, those residues interacting with the RNA backbone are the most conserved among known L25 sequences, whereas those interacting with the bases are not. In Escherichia coli, the 120-nt 5S rRNA binds specifically to three proteins, L25, L18 and L5, forming a separate domain of the ribosome (1). Ribosomal protein L25 binds specifically to a portion of 5S rRNA called loop E, which contains seven nonWatson-Crick base pairs stabilized in the protein-free RNA by several magnesium ions. The structure of the loop E duplex in the absence of protein is significantly distorted from canonical A form RNA (2). Both the hydrogen-bond donors and acceptors that are presented in a widened minor groove and the backbone structure of loop E differ from A form RNA. Its distorted structure is stabilized by a ''spine'' of Mg 2ϩ bound in the major groove. Further, the major groove of ''helix IV,'' which lies adjacent to loop E is likewise significantly widened, implying its potential accessibility to sequence-specific protein interactions. Biochemical protection, modification, and interference studies imply that L25 binds to the portion of 5S rRNA including the minor groove side of loop E and the adjacent major groove of helix IV (3-7).The high-resolution crystal or solution structures of about 16 ribosomal proteins or fragments thereof have been established (8), including the solution NMR structure of protein L25 (9). The structures of these and other ribosomal proteins in the context of the ribosome, where they may all make some interactions with RNA, are beginning to emerge at low resolution (10-12). The solution structure of protein L25 uncomplexed with RNA shows two significantly disordered loops and a ␤-barrel domain with significant structural similarities to the anti-codon-binding domains of E. coli glutaminyl-tRNA synthetase (13).Although aminoacyl-tRNA synthetases and sequence-specific DNA-binding proteins must discriminate among RNA and DNA substrates that have largely identical secondary and tertiary structures, ribosomal proteins might be expected to bind to RNA regions that have very distinctive structures as well as varied sequences. Consequently, the structural basis of RNA recognition by this category of proteins may include different features. Indeed, the very recent structure ...

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“…7 sites per sequence). Moreover, the abundance by itself is not the single criteria to determine the code word of interest (23). The highest proportion of triplet code-words discriminated by this analysis was found in the alpha and beta domains of the secondary structure of Actinomycetes as a product of the mutational bias induced by genomic GC pressure (Fig.…”

Section: Preferred Triplet Nucleotidesmentioning

confidence: 92%

“…The main binding sites of E. coli 5S RNA, the rpL5 and rpL18 proteins, are found in these domains with the hinge region conformation being critical for the initial recognition of rpL18 (9,10,14,18,23,24,34). Such a configuration seems to guarantee the conformation stability necessary for recognition.…”

Section: Triplet Words As Structural and Functional Lexical Motifsmentioning

confidence: 99%

The function of lexical motifs in the organization of the Actinomycetes 5S rRNAs

Rodrigues-Subacius¹,

Padilla²

2007

Braz. J. Microbiol.

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This work shows results obtained by employing the linguistic method to identify biologically meaningful sites in Actinomycetes 5S rRNAs. The approach adopted identifies triplet-words, along the base sequence of 5S rRNA, located mainly at the alpha and beta domains of the 5S secondary structure. There are triplet-words representing universal protein binding sites that include important prokaryote signatures, and sites strategically located in critical regions related to the formation of the 5S ribonucleoproteins (RNP) complex. In those sites, where the GC pressure promoted substitutions, the analysis demonstrates that alterations did not affect their biological significance. Sites formed by GGY (or more rarely GGR), continued to play an important role as ribosomal proteins rpL18 and rpL5 protein receptors. The data suggest that instead of increasing the molecular variability, expected for the diversity in species and habitats occupied for the group, GC pressure functioned as a reducer mechanism for the inter-specific diversity.

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5S rRNA sugar‐phosphate backbone protection in complexes with specific ribosomal proteins

Cited by 15 publications

References 18 publications

The NMR structure ofEscherichia coliribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases

The NMR structure ofEscherichia coliribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases

Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-Å resolution

The function of lexical motifs in the organization of the Actinomycetes 5S rRNAs

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