The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site α-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with β-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.
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http://dx.doi.org/10.1016/j.jsb.2012.02.006 | DOI Listing |
J Biol Chem
December 2024
Division of Biological Sciences, Indian Institute of Science, Bangalore 560 012. Electronic address:
Paralogues of the bifunctional nuclease, Ribonuclease J (RNase J) demonstrate varied catalytic efficiencies despite extensive sequence and structural similarity. Of the two S. aureus RNase J paralogues, RNase J1 is substantially more active than RNase J2.
View Article and Find Full Text PDFFront Microbiol
December 2024
Núcleo de Investigación en One Health, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile.
Type VI Secretion Systems (T6SS), widely distributed in Gram-negative bacteria, contribute to interbacterial competition and pathogenesis through the translocation of effector proteins to target cells. harbor 5 pathogenicity islands encoding T6SS (SPI-6, SPI-19, SPI-20, SPI-21 and SPI-22), in which a limited number of effector proteins have been identified. Previous analyses by our group focused on the identification of candidate T6SS effectors and cognate immunity proteins in genomes deposited in public databases.
View Article and Find Full Text PDFSheng Wu Gong Cheng Xue Bao
December 2024
College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China.
Argonaute proteins are active throughout the lifetime in a variety of organisms and they bind to small RNAs (sRNAs) to regulate gene expression. The Argonaute proteins of vertebrates can be classified into two clades: the Ago clade and the Piwi clade. Both clades have N, L1, L2, PAZ, MID and PIWI domains.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far.
View Article and Find Full Text PDFBMC Biol
December 2024
Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, Poznan, 61-704, Poland.
Background: Vertebrates have one Dicer ortholog that generates both microRNAs (miRNAs) and small interfering RNAs (siRNAs), in contrast to the multiple Dicer-like proteins found in flies and plants. Here, we focus on the functions of the human Dicer (hDicer) helicase domain. The helicase domain of hDicer is known to recognize pre-miRNA substrates through interactions with their apical loop regions.
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