Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family

Nevskaya, N.; Tischenko, Svetlana; Fedorov, Roman; Al-Karadaghi, Salam; Liljas, Anders; Kraft, A.; Piendl, Wolfgang; Garber, Maria; Nikonov, S.V.

doi:10.1016/s0969-2126(00)00116-7

Cited by 35 publications

(31 citation statements)

References 24 publications

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“…Therefore, having started from the known structures of L1 proteins from other organisms we built a model of HmaL1 and refined it by molecular dynamics methods (in press). This model was very close to the crystal structure of the L1 protein from Methanocaldococcus jannashchii (MjaL1) charged positively [10]. However, the crystal structures and mutual arrangement of HmaL1 and RNA moieties within the HmaL1 stalk remain unknown.…”

Section: Introductionsupporting

confidence: 70%

Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui

Габдулхаков¹,

Tishchenko²,

Mikhaylina³

et al. 2017

Crystals

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Abstract:The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma) has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function.

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Section: Introductionsupporting

confidence: 70%

Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui

Габдулхаков¹,

Tishchenko²,

Mikhaylina³

et al. 2017

Crystals

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“…As for L1, it has been proposed to be located on the opposite side of the ribosome from the stalk position (39,68). However, intrinsic flexibility of L1 has been suggested, depending on RNA binding (46)(47)(48); it adopts a closed conformation in the absence of RNA (47) but opens upon RNA binding (46,48). This probably explains the difficulty in precisely determining the structure of the L1 protuberance within the ribosome, due to the high mobility of the region (1,48).…”

Section: Discussionmentioning

confidence: 99%

Interactions of an EssentialBacillus subtilisGTPase, YsxC, with Ribosomes

et al. 2008

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YsxC is a small GTPase of Bacillus subtilis with essential but still unknown function, although recent works have suggested that it might be involved in ribosome biogenesis. Here, purified YsxC overexpressed in Escherichia coli was found to be partly associated with high-molecular-weight material, most likely rRNA, and thus eluted from gel filtration as a large complex. In addition, purification of ribosomes from an E. coli strain overexpressing YsxC allowed the copurification of the YsxC protein. Purified YsxC was shown to bind preferentially to the 50S subunit of B. subtilis ribosomes; this interaction was modulated by nucleotides and was stronger in the presence of a nonhydrolyzable GTP analogue than with GTP. Far-Western blotting analysis performed with His 6 -YsxC and ribosomal proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that YsxC interacted with at least four ribosomal proteins from the 50S subunit. Two of these putative protein partners were identified by mass spectrometry as L1 and L3, while the third reactive band in the one-dimensional gel contained L6 and L10. The fourth band that reacted with YsxC contained a mixture of three proteins, L7/L12, L23, and L27, suggesting that at least one of them binds to YsxC. Coimmobilization assays confirmed that L1, L6, and L7/L12 interact with YsxC. Together, these results suggest that YsxC plays a role in ribosome assembly.

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“…Also the 50S ribosomal subunit of the 70S ribosome structure seems to include some misinterpreted electron density regions. The trace of protein L1 C alpha atoms is partly overlapping with the trace of 23S rRNA phosphorus atoms (PDB code 1 giy) [5, 6] and the orientation of the two domains of L1 deviates from the one observed in L1 [7,8] or in its complex with rRNA [6]. …”

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confidence: 99%