Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30

Leijonmarck, Marie; Appelt, K.; Badger, John; Liljas, Anders; Wilson, K.S.; White, Stephen W.

doi:10.1002/prot.340030405

Cited by 20 publications

(10 citation statements)

References 24 publications

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“…Each domain of IF3 has an exposed f-sheet as part of an WJo topology. This motif is reminiscent of the structure of several ribosomal proteins (Wilson et al, 1986;Leijonmarck et al, 1988;Ramakrishnan and White, 1992;Golden et al, 1993) and the RNA binding protein UIA (Nagai et al, 1990;Hoffmann et al, 1991). The topology of the IF3 domains is not the same as in these proteins.…”

Section: Discussionmentioning

confidence: 99%

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

1995

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The structures of the two domains of translational initiation factor IF3 from Bacillus stearothermophilus have been solved by X‐ray crystallography using single wavelength anomalous scattering and multiwavelength anomalous diffraction. Each of the two domains has an alpha/beta topology, with an exposed beta‐sheet that is reminiscent of several ribosomal and other RNA binding proteins. An alpha‐helix that protrudes out from the body of the N‐terminal domain towards the C‐terminal domain suggests that IF3 consists of two RNA binding domains connected by an alpha‐helix and that it may bridge two regions of the ribosome. This represents the first high resolution structural information on a translational initiation factor.

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Section: Discussionmentioning

confidence: 99%

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

1995

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“…Although the L6 domain structure is unique, it is related to a structural motif seen in several other proteins from ribonucleoprotein particles. It has previously been shown that three small proteins, ribosomal proteins L7/L12 and L30 and the RNA binding domain of Ul snRNP A protein (A-RRM-1), have similar structures in which a-helices are packed against one surface of an anti-parallel (3-sheet (Leijonmarck et al, 1980(Leijonmarck et al, , 1988Wilson et al, 1986;Nagai et al, 1990;Hoffman et al, 1991). It was proposed that this similarity, which includes identical topologies and connectivities of secondary structural elements, might indicate a common evolutionary origin for these molecules (Wilson et al, 1986;Hoffman et al, 1991;Leijonmarck et al, 1988).…”

Section: Discussionmentioning

confidence: 99%

Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein.

1993

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In all cells, protein synthesis is coordinated by the ribosome, a large ribonucleoprotein particle that is composed of > 50 distinct protein molecules and several large RNA molecules. Here we present the crystal structure of ribosomal protein L6 from the thermophilic bacterium Bacillus stearothermophilus solved at 2.6 A resolution. L6 contains two domains with almost identical folds, implying that it was created by an ancient gene duplication event. The surface of the molecule displays several likely sites of interaction with other components of the ribosome. The RNA binding sites appear to be localized in the C‐terminal domain whereas the N‐terminal domain contains the potential sites for protein‐protein interactions. The domain structure is homologous with several other ribosomal proteins and to a large family of eukaryotic RNA binding proteins.

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“…A detailed structural analysis ofthe two ribosomal proteins concluded that their structural homology is a result of divergent evolution (36) (35,36). The diagram shown as the RRM represents the general structural features predicted for all members of the RRM family based upon primary sequence homologies (8).…”

Section: Discussionmentioning

confidence: 99%

RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins.

Hoffman

Query

Golden

et al. 1991

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

188

100

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An RNA recognition motif (RRM) of '480 amino acids constitutes the core of RNA-binding domains found in a large family of proteins involved in RNA processing.The Ul RNA-binding domain ofthe A protein component ofthe human Ul small nuclear ribonucleoprotein (RNP), which encompasses the RRM sequence, was analyzed by using NMR spectroscopy. The domain of the A protein is a highly stable monomer in solution consisting of four antiparallel f-strands and two a-helices. The highly conserved RNP1 and RNP2 consensus sequences, containing residues previously suggested to be involved in nucleic acid binding, are juxtaposed in adjacent f-strands. Conserved aromatic side chains that are critical for RNA binding are clustered on the surface of the molecule adjacent to a variable loop that influences recognition of specific RNA sequences. The secondary structure and topology of the RRM are similar to those of ribosomal proteins L12 and L30, suggesting a distant evolutionary relationship between these two types of RNA-associated proteins.Over the past decade, the ways in which proteins interact specifically and nonspecifically with DNA have been revealed by biochemical and biophysical studies (reviewed in refs. 1 and 2). Much of this information has been the result of crystallographic analysis, but more recently, NMR techniques have been used (3). As regards RNA-binding proteins, however, there has been little structural information with the notable exception of the work by Steitz and coworkers (4) on the glutaminyl-tRNA synthetase/tRNAGIn complex.Sequence elements characteristic of a group of RNAassociated proteins began to emerge with the observation of four copies of an 80-amino acid repeat in poly(A)-binding protein (5). The most conserved region of 8 amino acids in these repeats was termed the ribonucleoprotein (RNP) consensus sequence, or octamer (RNP1) (6). Another 6-amino acid region was later termed RNP2 (7). It was subsequently shown by several groups that the sequence similarity appears in many other RNA-associated proteins (7-11) (recently reviewed in ref. 12), contains many conserved positions, and is notably rich in aromatic residues (8). Direct evidence of an interaction between this motif and RNA has led to its designation as an RNA recognition motif, or RRM (8). This motif has also been referred to as an RNP consensus sequence-type RNA binding domain (11) and as an RNP-80 motif (13). Members of the RRM-containing family of proteins include heterogeneous nuclear RNP proteins and U-class small nuclear RNP (snRNP) proteins, as well as poly(A)-binding protein, nucleolin, transcription termination factors La and rho, eukaryotic initiation factor 4B, and sexdetermination proteins in Drosophila. The sources of these proteins range from Escherichia coli to man; thus, the RRM is clearly an ancient protein structure.The RRM can be viewed as analogous to the homeobox domain (5) or to the zinc-binding finger motif (14) of DNAbinding proteins. In many cases, the RRM is a modular component ofa larger protein; other m...

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Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30

Cited by 20 publications

References 24 publications

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein.

RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins.

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