Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein.

Hoffman, David W.; Davies, Christopher; Gerchman, Sue Ellen; Kycia, Jadwiga H.; Porter, Stephanie; White, Stephen W.; Ramakrishnan, V.

doi:10.1002/j.1460-2075.1994.tb06250.x

Cited by 108 publications

(130 citation statements)

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“…The structural motif first observed in the L30 and L7/L 12 structures has also been identified in L6, L9 and $6, and this supports the idea of a sub-family of related ribosomal proteins. The same motif has also been found in the U I RNA-binding domain of the U lsnRNP-A protein (Nagai, Oubridge, Jessen, Li & Evans, 1990;Hoffman, Query, Golden, White & Keene, 1991), which raises the interesting possibility that these RNA-associated proteins are derived from an ancient RNA-binding domain Hoffman et al, 1994).…”

Section: Introductionmentioning

confidence: 69%

“…Recently, the structures of several additional ribosomal proteins have been solved by NMR and protein crystallography. These are $5 (Ramakrishnan & White, 1992), S17 (Golden, Hoffman, Ramakrishnan & White, 1993), L6 , L9 (Hoffman et al, 1994) and $6 (Liljas, 1993). The structural motif first observed in the L30 and L7/L 12 structures has also been identified in L6, L9 and $6, and this supports the idea of a sub-family of related ribosomal proteins.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14

Davies¹,

Gerchman²,

Kycia³

et al. 1994

Acta Cryst D

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Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins. To verify this, the gene for Bacillus stearothermophUus L14 has been cloned, and the protein has been purified and crystallized. The crystals are in space group C2 with cell dimensions a = 67.0, b = 32.7, c = 49.4/~, and ,8 = 101.8 °, and there is one molecule in the asymmetric unit (V,,, = 2.0 A 3 Da -~). They are of high quality, and a native data set has been collected to a resolution of 1.6 t%, with an emerge of 5.3%.

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Section: Introductionmentioning

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14

Davies¹,

Gerchman²,

Kycia³

et al. 1994

Acta Cryst D

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“…The first high resolution structure of an SAH domain was revealed in a crystal structure of the Bacillus stearothermophilus ribosomal protein L9 (25). This protein contained a rigid and fully extended 34-amino acid linker region between two compact globular domains (Fig.…”

Section: Identification and Characterization Of Sah Domains In Naturamentioning

confidence: 99%

Harnessing the Unique Structural Properties of Isolated α-Helices

Swanson

Sivaramakrishnan

2014

Journal of Biological Chemistry

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The ␣-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of ␣-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single ␣-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ϳ4 consecutive glutamic acids followed by ϳ4 consecutive basic arginine or lysine (R/K) residues. The ER/K ␣-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells. Coiled-coil or Single ␣-Helical (SAH) Domain?Until recently, SAH 2 domains in natural proteins were predicted by secondary structure prediction algorithms to form a coiled-coil, in part due to the high concentration of charged and polar residues that are also the hallmark of the coiled-coil motif (1). Among the multiple folds in globular proteins that stabilize ␣-helices, the coiled-coil motif has been extensively characterized and in general is the most predictable form of tertiary protein structure (2). In the coiled-coil motif, two or more ␣-helices are individually stabilized by sequence-specific packing at consensus hydrophobic patches. Extensive studies have elicited general sequence and structure rules that govern coiled-coil interactions. Briefly, the amino acid sequence of each ␣-helix in a coiled-coil is divided into heptads (7 residues) that form nearly two complete ␣-helical turns and span 1.05 nm along the helical axis. Each amino acid in the heptad is described by its relative position, moving from the N to C terminus, using the nomenclature abcdefg. In canonical dimeric coiled-coils, the a and d positions radiate away from the core of the ␣-helix, 60°a part and offset by 0.45 nm along the helix length, and are typically occupied by aliphatic hydrophobic residues, whereas polar residues comprise the rest of the positions. As the heptad is repeated, it forms a continuous hydrophobic patch located along a single face of the ␣-helix compatible with a tight intermolecular interaction between polypeptides with the same or similar heptad pattern (2). However, often polar or charged residues occupy the a and d positions, leading to local destabilization of the coiled-coil...

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“…Protein L9 provides an example of such asymmetry in the ribosome. The crystal structure (58) shows two RNA-binding globular domains linked by an exposed ␣-helix, yielding a protein that is 82 Å long. IEM places an epitope of L9 near the L1 shoulder, but antibody binding most strongly affects activities at the translocational domain, between the central protuberance and the base of the L7/L12 stalk (59).…”

Section: Reconstitution Of 50 S Subunits With [ 3 H]dnp-l23-50mentioning

confidence: 99%

Incorporation of Dinitrophenyl Protein L23 into Totally Reconstituted Escherichia coli 50 S Ribosomal Subunits and Its Localization at Two Sites by Immune Electron Microscopy

Montesano-Roditis¹,

Glitz²,

Perrault³

et al. 1997

Journal of Biological Chemistry

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Escherichia coli ribosomal protein L23 was derivatized with [ 3 H]2,4-dinitrofluorobenzene both at the N terminus and at internal lysines. Dinitrophenyl-L23 (DNP-L23) was taken up into 50 S subunits from a reconstitution mixture containing rRNA and total 50 S protein depleted in L23. Unmodified L23 competed with DNP-L23 for uptake, indicating that each protein form bound in an identical or similar position within the subunit. Modified L23, incorporated at a level of 0.7 or 0.4 DNP groups per 50 S, was localized by electron microscopy of subunits complexed with antibodies to dinitrophenol. Antibodies were seen at two major sites with almost equal frequency. One site is beside the central protuberance, in a region previously identified as the peptidyltransferase center. The second location is at the base of the subunit, in the area of the exit site from which the growing peptide leaves the ribosome. Models derived from image reconstruction show hollows or canyons in the subunit and a tunnel that links the transferase and exit sites. Our results indicate that L23 is at the subunit interior, with separate elements of the protein at the subunit surface at or near both ends of this tunnel.Determination of the positions of proteins within the 30 S and 50 S ribosomal subunits has been a major goal of studies directed toward the elucidation of the structure and function of the Escherichia coli ribosome. The technique of immune electron microscopy (IEM), 1 the visualization in electron micrographs of complexes formed between ribosomal subunits and specific antibodies, has been especially useful for this purpose (1, 2). However, in the case of protein L23, application of IEM has yielded controversial results. The object of the present work is to resolve this controversy.E. coli ribosomal protein L23 is a primary binding protein; it interacts directly with ribosomal RNA (3) and plays a significant role in the assembly of the large ribosomal subunit (4). The protein has been linked to the ribosomal peptidyltransferase center in several ways. First, photoaffinity labeling of 70 S ribosomes with either puromycin (5-7) or p-azidopuromycin (8, 9), each of which inhibits protein synthesis by acting as a peptide acceptor in the transferase reaction, led to photoincorporation into L23 as the major site of protein labeling. Second, antibodies recognizing the N 6 ,N 6 -dimethyladenosine moiety of puromycin bound to labeled 50 S subunits in a region generally agreed to include the peptidyltransferase center, i.e. between the central protuberance and the site of protein L1, near the 30 S:50 S interface (10, 11). Third, chemical cross-linking and related studies showed L23 to neighbor other proteins (L2, L15, L16, and L27) that have been placed at or near the peptidyltransferase center (12). Finally, although peptidyltransferase activity is not altered in reconstituted 50 S subunits either lacking L23 or including puromycin-modified L23 in place of L23, the latter do show reduced aminoacyl-tRNA binding (6), which suggests proximity to t...

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Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein.

Cited by 108 publications

References 50 publications

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14

Harnessing the Unique Structural Properties of Isolated α-Helices

Incorporation of Dinitrophenyl Protein L23 into Totally Reconstituted Escherichia coli 50 S Ribosomal Subunits and Its Localization at Two Sites by Immune Electron Microscopy

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