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

Crystals ◽  
2017 ◽  
Vol 7 (2) ◽  
pp. 37 ◽  
Author(s):  
Azat Gabdulkhakov ◽  
Svetlana Tishchenko ◽  
Alisa Mikhaylina ◽  
Maria Garber ◽  
Natalia Nevskaya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
23S Rrna ◽  
Haloarcula Marismortui

scholarly journals Crystal Structure of Escherichia coli-Expressed Haloarcula marismortui Bacteriorhodopsin I in the Trimeric Form

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e112873 ◽  
Author(s):  
Vitaly Shevchenko ◽  
Ivan Gushchin ◽  
Vitaly Polovinkin ◽  
Ekaterina Round ◽  
Valentin Borshchevskiy ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Haloarcula Marismortui

The 2.0 Å crystal structure of catalase-peroxidase from Haloarcula marismortui

2002 ◽  
Vol 9 (9) ◽  
pp. 691-695 ◽  
Author(s):  
Yusuke Yamada ◽  
Taketomo Fujiwara ◽  
Takao Sato ◽  
Noriyuki Igarashi ◽  
Nobuo Tanaka
Keyword(s):  
Crystal Structure ◽  
Haloarcula Marismortui ◽  
Catalase Peroxidase

scholarly journals Transcription Analysis of Two Disparate rRNA Operons in the Halophilic Archaeon Haloarcula marismortui

1998 ◽  
Vol 180 (18) ◽  
pp. 4804-4813 ◽  
Author(s):  
Patrick P. Dennis ◽  
Sonia Ziesche ◽  
Shanthini Mylvaganam
Keyword(s):  
16S Rrna ◽  
Sequence Divergence ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Processing ◽  
Halophilic Archaeon ◽  
Haloarcula Marismortui ◽  
Transcription Analysis ◽  
Flanking Sequences ◽  
Flanking Regions

ABSTRACT The genome of the halophilic archaeon Haloarcula marismortui contains two rRNA operons designated rrnAand rrnB. Genomic clones of the two operons and their flanking regions have been sequenced, and primary transcripts and processing intermediates derived from each operon have been characterized. The 16S, 23S, and 5S genes from the two operons were found to differ at 74 of 1,472 positions, 39 of 2,922 positions, and 2 of 122 positions, respectively. This degree of sequence divergence for multicopy (paralogous) rRNA genes was 10- to 50-fold or more higher than anticipated. The two operons exhibit other profound differences that include (i) the presence in rrnA and the absence inrrnB of tRNAAla and tRNACys genes in the intergenic and distal regions, respectively, (ii) divergent 5′ flanking sequences, and (iii) distinct pathways for processing and maturation of 16S rRNA. Processing and maturation of 16S and 23S rRNA from rrnA operon transcripts and of 23S rRNA fromrrnB operon transcripts follow the canonical halophilic pathway, whereas maturation of 16S rRNA from rrnB operon transcripts follows an unusual and different pathway that is apparently devoid of any 5′ processing intermediate.

scholarly journals Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alena Stsiapanava ◽  
Maria Selmer
Keyword(s):  
Crystal Structure ◽  
Tertiary Structure ◽  
Catalytic Domain ◽  
Antibiotic Resistance Genes ◽  
Macrolide Resistance ◽  
Saccharopolyspora Erythraea ◽  
23S Rrna ◽  
Cofactor Binding ◽  
Sequence Identity ◽  
Adenosyl Methionine

Abstract Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC’ that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC’ in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC’ by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.

Domain Organization and Crystal Structure of the Catalytic Domain of E.coli RluF, a Pseudouridine Synthase that Acts on 23S rRNA

2006 ◽  
Vol 359 (4) ◽  
pp. 998-1009 ◽  
Author(s):  
S. Sunita ◽  
H. Zhenxing ◽  
J. Swaathi ◽  
Miroslaw Cygler ◽  
Allan Matte ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
23S Rrna ◽  
Domain Organization ◽  
Pseudouridine Synthase

The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold

2002 ◽  
Vol 363 (3) ◽  
pp. 553-561 ◽  
Author(s):  
Esmeralda A. WOESTENENK ◽  
George M. GONGADZE ◽  
Dmitry V. SHCHERBAKOV ◽  
Alexey V. RAK ◽  
Maria B. GARBER ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Solution Structure ◽  
Rna Binding ◽  
Large Subunit ◽  
Thermus Thermophilus ◽  
23S Rrna ◽  
Haloarcula Marismortui ◽  
Globular Structure ◽  
High Resolution Structure ◽  
Rna Motif

We have determined the solution structure of ribosomal protein L18 from Thermus thermophilus. L18 is a 12.5kDa protein of the large subunit of the ribosome and binds to both 5S and 23S rRNA. In the uncomplexed state L18 folds to a mixed α/β globular structure with a long disordered N-terminal region. We compared our high-resolution structure with RNA-complexed L18 from Haloarcula marismortui and T. thermophilus to examine RNA-induced as well as species-dependent structural differences. We also identified T. thermophilus S11 as a structural homologue and found that the structures of the RNA-recognition sites are conserved. Important features, for instance a bulge in the RNA-contacting β-sheet, are conserved in both proteins. We suggest that the L18 fold recognizes a specific RNA motif and that the resulting RNA—protein-recognition module is tolerant to variations in sequence.

scholarly journals Crystal structure of RlmM, the 2′O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA

2012 ◽  
Vol 40 (20) ◽  
pp. 10507-10520 ◽  
Author(s):  
Avinash S. Punekar ◽  
Tyson R. Shepherd ◽  
Josefine Liljeruhm ◽  
Anthony C. Forster ◽  
Maria Selmer
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
23S Rrna

scholarly journals Mutations in the GTPase Center of Escherichia coli 23S rRNA Indicate Release Factor 2-Interactive Sites

2002 ◽  
Vol 184 (4) ◽  
pp. 1200-1203 ◽  
Author(s):  
Wenbing Xu ◽  
Frances T. Pagel ◽  
Emanuel J. Murgola
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Translation Termination ◽  
23S Rrna ◽  
Release Factor ◽  
Suppressor Activity ◽  
Suppressor Mutations ◽  
Nonsense Suppressors

ABSTRACT Mutations in the GTPase center of Escherichia coli 23S rRNA were characterized in vivo as UGA-specific nonsense suppressors. Some site-directed mutations did not exhibit suppressor activity and were interspersed among suppressor mutations. Our results demonstrate the involvement of the two adjacent loops of this conserved rRNA structure in UGA-dependent translation termination and, taken with previous in vitro analyses and with consideration of the crystal structure of the GTPase center RNA, indicate that nucleotides 1067, 1093, 1094, and 1095 are sites of interaction with release factor 2.

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