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

Abstract

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.

Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

“… 93 ) for bL31, 5ML7 (ref. 94 ) and 3U4M 95 were used for the L1 stalk region, 5AFI 96 and 5UYQ 97 were used for tRNAs, and 6QNQ was used to help tentatively place metal ions 98 . PDB 5LI0 (ref.…”

Structural basis of resistance to lincosamide, streptogramin A, and pleuromutilin antibiotics by ABCF ATPases in Gram-positive pathogens

“…For the E. faecalis and L. monocytogenes ribosomes, homology models were generated with SWISS-MODEL (Waterhouse et al , 2018), mostly from PDB 6HA1/6HA8 (Crowe-McAuliffe et al ., 2018). PDBs 4YBB (Noeske et al , 2015) 5MDV (James et al , 2016) were used as additional templates and references where necessary, 4V9O (Pulk & Cate, 2013) was used for bS21, 5ML7 (Gabdulkhakov et al , 2017) and 3U4M (Tishchenko et al , 2012) were used for the L1 stalk region, 5AFI (Fischer et al , 2015) and 5UYQ (Loveland et al , 2017) were used for tRNAs, and 6QNQ was used to help placing metal ions (Rozov et al , 2019). PDB 5LI0 (Khusainov et al ., 2016) was used as a starting model for the S. aureus ribosome.…”

Intrinsic Disorder-Based Design of Stable Globular Proteins

“…Two ribosomal proteins L1 were chosen for this study, L1 from the halophilic archaeon Haloarcula marismortui (HmaL1) and L1 from the extremophilic bacterium Aquifex aeolicus (AaeL1). The three-dimensional structure of AaeL1 is known from the experiments [43]; for HmaL1, a homology model was built [44]. Both proteins have highly conservative three-dimensional structure specific for ribosome L1 proteins, which can be divided into two domains.…”