Endoribonucleases
Ribonuclease III
Substrate Specificity
RNA, Bacterial
Base Sequence
Escherichia coli
Molecular Sequence Data
Rpp14 and Rpp29, two protein subunits of human ribonuclease P. (1/2636)
In HeLa cells, the tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. Five of these proteins (hPop1p, Rpp20, Rpp30, Rpp38, and Rpp40) have been partially characterized. Here we report on the cDNA cloning and immunobiochemical analysis of Rpp14 and Rpp29. Polyclonal rabbit antibodies raised against recombinant Rpp14 and Rpp29 recognize their corresponding antigens in HeLa cells and precipitate catalytically active RNase P. Rpp29 shows 23% identity with Pop4p, a subunit of yeast nuclear RNase P and the ribosomal RNA processing enzyme RNase MRP. Rpp14, by contrast, exhibits no significant homology to any known yeast gene. Thus, human RNase P differs in the details of its protein composition, and perhaps in the functions of some of these proteins, from the yeast enzyme. (+info)The 3' end CCA of mature tRNA is an antideterminant for eukaryotic 3'-tRNase. (2/2636)
Cytoplasmic tRNAs undergo posttranscriptional 5' and 3' end processing in the eukaryotic nucleus, and CCA (which forms the mature 3' end of all tRNAs) must be added by tRNA nucleotidyl transferase before tRNA can be aminoacylated and utilized in translation. Eukaryotic 3'-tRNase can endonucleolytically remove a 3' end trailer by cleaving on the 3' side of the discriminator base (the unpaired nucleotide 3' of the last base pair of the acceptor stem). This reaction proceeds despite a wide range in length and sequence of the 3' end trailer, except that mature tRNA containing the 3' terminal CCA is not a substrate for mouse 3'-tRNase (Nashimoto, 1997, Nucleic Acids Res 25:1148-1154). Herein, we extend this result with Drosophila and pig 3'-tRNase, using Drosophila melanogaster tRNAHis as substrate. Mature tRNA is thus prevented from recycling through 3' end processing. We also tested a series of tRNAs ending at the discriminator base (-), with one C added (+C), two Cs added (+CC), and CCA added (+CCA) as 3'-tRNase inhibitors. Inhibition was competitive with both Drosophila and pig 3'-tRNase. The product of the 3'-tRNase reaction (-) is a good 3'-tRNase inhibitor, with a KI approximately two times KM for the normal 3'-tRNase substrate. KI increases with each nucleotide added beyond the discriminator base, until when tRNA+CCA is used as inhibitor, KI is approximately forty times the substrate KM. The 3'-tRNase can thus remain free to process precursors with 3' end trailers because it is barely inhibited by tRNA+CCA, ensuring that tRNA can progress to aminoacylation. The active site of 3'-tRNase may have evolved to make an especially poor fit with tRNA+CCA. (+info)Interaction of 5-lipoxygenase with cellular proteins. (3/2636)
5-Lipoxygenase (5LO) plays a pivotal role in cellular leukotriene synthesis. To identify proteins interacting with human 5LO, we used a two-hybrid approach to screen a human lung cDNA library. From a total of 1.5 x 10(7) yeast transformants, nine independent clones representing three different proteins were isolated and found to specifically interact with 5LO. Four 1.7- to 1.8-kb clones represented a 16-kDa protein named coactosin-like protein for its significant homology with coactosin, a protein found to be associated with actin in Dictyostelium discoideum. Coactosin-like protein thus may provide a link between 5LO and the cytoskeleton. Two other yeast clones of 1.5 kb encoded transforming growth factor (TGF) type beta receptor-I-associated protein 1 partial cDNA. TGF type beta receptor-I-associated protein 1 recently has been reported to associate with the activated form of the TGF beta receptor I and may be involved in the TGF beta-induced up-regulation of 5LO expression and activity observed in HL-60 and Mono Mac 6 cells. Finally, three identical 2.1-kb clones contained the partial cDNA of a human protein with high homology to a hypothetical helicase K12H4. 8 from Caenorhabditis elegans and consequently was named DeltaK12H4. 8 homologue. Analysis of the predicted amino acid sequence revealed the presence of a RNase III motif and a double-stranded RNA binding domain, indicative of a protein of nuclear origin. The identification of these 5LO-interacting proteins provides additional approaches to studies of the cellular functions of 5LO. (+info)Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. (4/2636)
Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed. (+info)Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution. (5/2636)
A variant of bovine pancreatic ribonuclease A has been prepared with seven amino acid substitutions (Q55K, N62K, A64T, Y76K, S80R, E111G, N113K). These substitutions recreate in RNase A the basic surface found in bovine seminal RNase, a homologue of pancreatic RNase that diverged some 35 million years ago. Substitution of a portion of this basic surface (positions 55, 62, 64, 111 and 113) enhances the immunosuppressive activity of the RNase variant, activity found in native seminal RNase, while substitution of another portion (positions 76 and 80) attenuates the activity. Further, introduction of Gly at position 111 has been shown to increase the catalytic activity of RNase against double-stranded RNA. The variant and the wild-type (recombinant) protein were crystallized and their structures determined to a resolution of 2.0 A. Each of the mutated amino acids is seen in the electron density map. The main change observed in the mutant structure compared with the wild-type is the region encompassing residues 16-22, where the structure is more disordered. This loop is the region where the polypeptide chain of RNase A is cleaved by subtilisin to form RNase S, and undergoes conformational change to allow residues 1-20 of the RNase to swap between subunits in the covalent seminal RNase dimer. (+info)Cloning and characterization of a mammalian pseudouridine synthase. (6/2636)
This report describes the cloning and characterization of a pseudouridine (psi) synthase from mouse that we have named mouse pseudouridine synthase 1 (mpus1p). The cDNA is approximately 1.5 kb and when used as a probe on a Northern blot of mouse RNA from tissues and cultured cells, several bands were detected. The open reading frame is 393 amino acids and has 35% identity over its length with yeast psi synthase 1 (pus1p). The recombinant protein was expressed in Escherichia coli and the purified protein converted specific uridines to psi in a number of tRNA substrates. The positions modified in stoichiometric amounts in vitro were 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA. A human cDNA was also cloned and the smaller open reading frame (348 amino acids) was 92% identical over its length with mpus1p but is shorter by 45 amino acids at the amino terminus. The expressed recombinant human protein has no activity on any of the tRNA substrates, most probably the result of the truncated open reading frame. (+info)Key role of barstar Cys-40 residue in the mechanism of heat denaturation of bacterial ribonuclease complexes with barstar. (7/2636)
The mechanism by which barnase and binase are stabilized in their complexes with barstar and the role of the Cys-40 residue of barstar in that stabilization have been investigated by scanning microcalorimetry. Melting of ribonuclease complexes with barstar and its Cys-82-Ala mutant is described by two 2-state transitions. The lower-temperature one corresponds to barstar denaturation and the higher-temperature transition to ribonuclease melting. The barstar mutation Cys-40-Ala, which is within the principal barnase-binding region of barstar, simplifies the melting to a single 2-state transition. The presence of residue Cys-40 in barstar results in additional stabilization of ribonuclease in the complex. (+info)Analysis of mutations in the yeast mRNA decapping enzyme. (8/2636)
A major mechanism of mRNA decay in yeast is initiated by deadenylation, followed by mRNA decapping, which exposes the transcript to 5' to 3' exonucleolytic degradation. The decapping enzyme that removes the 5' cap structure is encoded by the DCP1 gene. To understand the function of the decapping enzyme, we used alanine scanning mutagenesis to create 31 mutant versions of the enzyme, and we examined the effects of the mutations both in vivo and in vitro. Two types of mutations that affected mRNA decapping in vivo were identified, including a temperature-sensitive allele. First, two mutants produced decapping enzymes that were defective for decapping in vitro, suggesting that these mutated residues are required for enzymatic activity. In contrast, several mutants that moderately affected mRNA decapping in vivo yielded decapping enzymes that had at least the same specific activity as the wild-type enzyme in vitro. Combination of alleles within this group yielded decapping enzymes that showed a strong loss of function in vivo, but that still produced fully active enzymes in vitro. This suggested that interactions of the decapping enzyme with other factors may be required for efficient decapping in vivo, and that these particular mutations may be disrupting such interactions. Interestingly, partial loss of decapping activity in vivo led to a defect in normal deadenylation-dependent decapping, but it did not affect the rapid deadenylation-independent decapping triggered by early nonsense codons. This observation suggested that these two types of mRNA decapping differ in their requirements for the decapping enzyme. (+info)Endoribonucleases are enzymes that cleave RNA molecules internally, meaning they cut the phosphodiester bond between nucleotides within the RNA chain. These enzymes play crucial roles in various cellular processes, such as RNA processing, degradation, and quality control. Different endoribonucleases recognize specific sequences or structural features in RNA substrates, allowing them to target particular regions for cleavage. Some well-known examples of endoribonucleases include RNase III, RNase T1, and RNase A, each with distinct substrate preferences and functions.
Ribonucleases (RNases) are a group of enzymes that catalyze the degradation of ribonucleic acid (RNA) molecules by hydrolyzing the phosphodiester bonds. These enzymes play crucial roles in various biological processes, such as RNA processing, turnover, and quality control. They can be classified into several types based on their specificities, mechanisms, and cellular localizations.
Some common classes of ribonucleases include:
1. Endoribonucleases: These enzymes cleave RNA internally, at specific sequences or structural motifs. Examples include RNase A, which targets single-stranded RNA; RNase III, which cuts double-stranded RNA at specific stem-loop structures; and RNase T1, which recognizes and cuts unpaired guanosine residues in RNA molecules.
2. Exoribonucleases: These enzymes remove nucleotides from the ends of RNA molecules. They can be further divided into 5'-3' exoribonucleases, which degrade RNA starting from the 5' end, and 3'-5' exoribonucleases, which start at the 3' end. Examples include Xrn1, a 5'-3' exoribonuclease involved in mRNA decay; and Dis3/RRP6, a 3'-5' exoribonuclease that participates in ribosomal RNA processing and degradation.
3. Specific ribonucleases: These enzymes target specific RNA molecules or regions with high precision. For example, RNase P is responsible for cleaving the 5' leader sequence of precursor tRNAs (pre-tRNAs) during their maturation; and RNase MRP is involved in the processing of ribosomal RNA and mitochondrial RNA molecules.
Dysregulation or mutations in ribonucleases have been implicated in various human diseases, such as neurological disorders, cancer, and viral infections. Therefore, understanding their functions and mechanisms is crucial for developing novel therapeutic strategies.
Ribonuclease III, also known as RNase III or double-stranded RNA specific endonuclease, is an enzyme that belongs to the endoribonuclease family. This enzyme is responsible for cleaving double-stranded RNA (dsRNA) molecules into smaller fragments of approximately 20-25 base pairs in length. The resulting fragments are called small interfering RNAs (siRNAs), which play a crucial role in the regulation of gene expression through a process known as RNA interference (RNAi).
Ribonuclease III functions by recognizing and binding to specific stem-loop structures within dsRNA molecules, followed by cleaving both strands at precise locations. This enzyme is highly conserved across various species, including bacteria, yeast, plants, and animals, indicating its fundamental role in cellular processes. In addition to its involvement in RNAi, ribonuclease III has been implicated in the maturation of other non-coding RNAs, such as microRNAs (miRNAs) and transfer RNAs (tRNAs).
Substrate specificity in the context of medical biochemistry and enzymology refers to the ability of an enzyme to selectively bind and catalyze a chemical reaction with a particular substrate (or a group of similar substrates) while discriminating against other molecules that are not substrates. This specificity arises from the three-dimensional structure of the enzyme, which has evolved to match the shape, charge distribution, and functional groups of its physiological substrate(s).
Substrate specificity is a fundamental property of enzymes that enables them to carry out highly selective chemical transformations in the complex cellular environment. The active site of an enzyme, where the catalysis takes place, has a unique conformation that complements the shape and charge distribution of its substrate(s). This ensures efficient recognition, binding, and conversion of the substrate into the desired product while minimizing unwanted side reactions with other molecules.
Substrate specificity can be categorized as:
1. Absolute specificity: An enzyme that can only act on a single substrate or a very narrow group of structurally related substrates, showing no activity towards any other molecule.
2. Group specificity: An enzyme that prefers to act on a particular functional group or class of compounds but can still accommodate minor structural variations within the substrate.
3. Broad or promiscuous specificity: An enzyme that can act on a wide range of structurally diverse substrates, albeit with varying catalytic efficiencies.
Understanding substrate specificity is crucial for elucidating enzymatic mechanisms, designing drugs that target specific enzymes or pathways, and developing biotechnological applications that rely on the controlled manipulation of enzyme activities.
Bacterial RNA refers to the genetic material present in bacteria that is composed of ribonucleic acid (RNA). Unlike higher organisms, bacteria contain a single circular chromosome made up of DNA, along with smaller circular pieces of DNA called plasmids. These bacterial genetic materials contain the information necessary for the growth and reproduction of the organism.
Bacterial RNA can be divided into three main categories: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). mRNA carries genetic information copied from DNA, which is then translated into proteins by the rRNA and tRNA molecules. rRNA is a structural component of the ribosome, where protein synthesis occurs, while tRNA acts as an adapter that brings amino acids to the ribosome during protein synthesis.
Bacterial RNA plays a crucial role in various cellular processes, including gene expression, protein synthesis, and regulation of metabolic pathways. Understanding the structure and function of bacterial RNA is essential for developing new antibiotics and other therapeutic strategies to combat bacterial infections.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
'Escherichia coli' (E. coli) is a type of gram-negative, facultatively anaerobic, rod-shaped bacterium that commonly inhabits the intestinal tract of humans and warm-blooded animals. It is a member of the family Enterobacteriaceae and one of the most well-studied prokaryotic model organisms in molecular biology.
While most E. coli strains are harmless and even beneficial to their hosts, some serotypes can cause various forms of gastrointestinal and extraintestinal illnesses in humans and animals. These pathogenic strains possess virulence factors that enable them to colonize and damage host tissues, leading to diseases such as diarrhea, urinary tract infections, pneumonia, and sepsis.
E. coli is a versatile organism with remarkable genetic diversity, which allows it to adapt to various environmental niches. It can be found in water, soil, food, and various man-made environments, making it an essential indicator of fecal contamination and a common cause of foodborne illnesses. The study of E. coli has contributed significantly to our understanding of fundamental biological processes, including DNA replication, gene regulation, and protein synthesis.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
Endoribonuclease - Wikipedia
It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly
Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15 Reveal Insight Into Nuclease Specificity and Dynamics
Swt1 MGI Mouse Gene Detail - MGI:1914125 - SWT1 RNA endoribonuclease homolog (S. cerevisiae)
Plus it
endoribonuclease activity, cleaving miRNA-paired mRNA Antibodies | Invitrogen ...
Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease | Lund University...
Human Serine/threonine-protein kinase/endoribonuclease IRE1 (ERN1)
Structural biology of SARS-CoV-2 Endoribonuclease NendoU (nsp15) » inside corona
Figure - Viral Interference between Respiratory Viruses - Volume 28, Number 2-February 2022 - Emerging Infectious Diseases...
Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. - Centre for Medicines...
RMRP gene: MedlinePlus Genetics
Abce1 ATP-binding cassette, sub-family E member 1 [Mus musculus (house mouse)] - Gene - NCBI
Nutrients | Free Full-Text | Effects of Three-Month Administration of High-Saturated Fat Diet and High-Polyunsaturated Fat...
XBP1 | Cancer Genetics Web
Inducing circular RNA formation using the CRISPR endoribonuclease Csy4. | RNA;23(5): 619-627, 2017 05. | MEDLINE |...
6QY3: Segment of the Cas1-Cas2-Csn2-DNA filament complex from the Type II-A CRISPR-Cas system
Ribosome maturation by the endoribonuclease YbeY stabilises a type III secretion system transcript required for virulence of...
Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity | Scientific Reports
Structural basis for RNA slicing by a plant Argonaute | Nature Structural & Molecular Biology
ENDOU | Cancer Genetics Web
Frontiers | Pangolins Lack IFIH1/MDA5, a Cytoplasmic RNA Sensor That Initiates Innate Immune Defense Upon Coronavirus Infection
SCOPe 2.08: Domain d2rhbc1: 2rhb C:1-190
Publications: Max Planck Institute of Molecular Cell Biology and Genetics
MBS1430578 | Recombinant Rhodopseudomonas palustris Probable rRNA maturation factor (RPC 0470)
The Emerging Perspective of Morphine Tolerance: MicroRNAs
Frontiers | RNase T2 in Inflammation and Cancer: Immunological and Biological Views
사)한국미생물학회
Agronomy | Free Full-Text | CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments
Nsp154
- Here we report the high-resolution crystal structure of endoribonuclease Nsp15/NendoU from SARS-CoV-2 - a virus causing current world-wide epidemics. (biorxiv.org)
- The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. (lu.se)
- The SARS-CoV-2's endoribonuclease (NendoU) nsp15, is an Mn 2+ dependent endoribonuclease specific to uridylate that SARS-CoV-2 uses to avoid the innate immune response by managing the stray RNA generated during replication. (insidecorona.net)
- One of these non-structural proteins is nsp15, a 346 amino acid nidoviral RNA uridylate‐specific and Mn 2+ -dependent [3] endoribonuclease (NendoU). (insidecorona.net)
Enzyme2
- Several proteins attach (bind) to this RNA molecule, forming an enzyme called mitochondrial RNA-processing endoribonuclease, or RNase MRP. (medlineplus.gov)
- And the whole operation is completed when NOB1, an endoribonuclease enzyme, cuts the rRNA at a specific site. (uni-muenchen.de)
Ribonuclease1
- An endoribonuclease is a ribonuclease endonuclease. (wikipedia.org)
Cleaves1
- These oligonucleotides activate an endoribonuclease (RNase L) which cleaves single-stranded RNA. (umassmed.edu)
Ribosome1
- The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. (nih.gov)
Activity2
- The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task. (bvsalud.org)
- AtAgo10 slicing activity is licensed by docking target (t) nucleotides t9-t13 into a surface channel containing the AGO endoribonuclease active site. (nature.com)
Found1
- Further examples include endoribonuclease XendoU found in frogs (Xenopus). (wikipedia.org)
Formation1
- Inducing circular RNA formation using the CRISPR endoribonuclease Csy4. (bvsalud.org)
Dicer3
- Dicer is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. (thermofisher.com)
- Long dsRNAs are degraded by the endoribonuclease Dicer into small effector molecules called siRNAs (small interfering RNAs). (idtdna.com)
- its product, dicer protein, is a ribonuclease (RNase) III endoribonuclease which is essential for the production of microRNAs (miRNA) which are formed by the cleavage of pre-miRNA or double-stranded RNA1-4. (hypothes.is)
Homolog1
- Here, we first show that SoxR of Acinetobacter oleivorans displayed similar activation profiles in response to RACs as did its homolog from Escherichia coli but controlled a different set of target genes, including sinE, which encodes an endoribonuclease. (korea.ac.kr)
ENZYME2
MRNA1
- Endoribonuclease active on single-stranded mRNA. (nih.gov)
RNAse2
Toxin3
- Bacterial endoribonuclease toxins in the toxin-antitoxin systems. (bmbreports.org)
- The types of toxin-antitoxin systems are determined by how antitoxins antagonize the endoribonuclease toxins. (bmbreports.org)
- In type III toxin-antitoxin systems, antitoxins are small noncoding RNAs that are transcribed as longer transcripts and then processed by the cognate endoribonuclease toxin into 34-36 nt sRNAs. (bmbreports.org)
Cleavage1
- Here, we identify an endoribonuclease, precursor of 21U RNA 5′-end cleavage holoenzyme (PUCH), that initiates piRNA processing in the nematode Caenorhabditis elegans . (nature.com)
Complex1
- This protein encoded by this gene, when complexed with translin-associated protein X, also forms a Mg ion-dependent endoribonuclease that promotes RNA-induced silencing complex (RISC) activation. (nih.gov)