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evolution
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reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
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reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
Halalkalibacterium halodurans
ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids
evolution
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RNaseH enzymes belong to the nucleotidyl transferase superfamily whose members share a similar protein fold and catalytic mechanism
evolution
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the reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
malfunction
mutations in each of the three RNase H2 subunits are implicated in a human auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
malfunction
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strains deficient in RNase H2 display a weak mutator phenotype which is consistent with a defect in DNA repair. RNase H2 defects cause alterations in the timing of cell cycle transitions
malfunction
deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
malfunction
DELTArnhA and DELTArnhC are synthetically lethal
malfunction
DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
malfunction
disease-causing mutations impairs the process of RNase H1 direction of origin-specific initiation of DNA replication in human mitochondria. Depletion of RNase H1 causes a reduction in mtDNA level. In an RNase H1-deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. Impaired RNase H1 activity changes replication initiation in vivo. Effects of disease causing mutations in RNASEH1, which are associated with adult-onset mitochondrial encephalomyopathy, phenotype and mechanism, overview
malfunction
disrupting the activity of the two enzymes RNase H1 and H2 (rnh1DELTA rnh201DELTA in Saccharomyces cerevisiae) is a useful tool for increasing the persistence of DNA:RNA hybrids and studying the effects of hybrid-induced instability. In the absence of RNase H activity, the levels of hybrids formed at susceptible loci increase dramatically. This increase in hybrids is associated with increased rates of genome instability that include loss of heterozygosity (LOH) events, loss of entire chromosomes, and recombination at the ribosomal locus. rnh1DELTA rnh201DELTA mutants display an increase in Rad52-GFP foci. Cells lacking RNase H1 and H2 have a larger fraction of persistent R-loop induced damage than wild-type cells or cells lacking only one of the RNases H, failure to observe accumulating foci early in the cell cycle, phenotype, overview
malfunction
disruption of the rnhA gene has been reported to increase a basal level of SOS expression in Escherichia coli, probably due to persistence of R-loops on the chromosome
malfunction
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inhibition of hepatitis B virus (HBV) replication by N-hydroxyisoquinolinedione and N-hydroxypyridinedione ribonuclease H inhibitors. Blocking the HBV RNaseH activity prevents removal of the RNA strand from the minus-polarity DNA strand, resulting in an accumulation of RNA:DNA heteroduplexes
malfunction
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mice deficient in RNase H1 that localizes to mitochondria die during embryogenesis, probably due to the defective processing of R-loops. RNase H2 knockout mice are also not viable, and mutations in either of the human genes can cause Aicardi-Goutieres Syndrome, a severe inheritable neurodevelopmental disorder. In this disease, uncleaved RNA-DNA hybrids accumulate within cells that possibly upregulate interferon via the nucleic acid sensor cyclic GMP-AMP synthase (cGAS) and its adaptor protein STING
malfunction
pathogenic consequences of disease causing mutations in RNase H1, overview. Loss of RNase H1 leads to primer retention at both OriH and OriL. RNase H1 mutations associated with mtDNA replication defects are identified in patients with mitochondrial encephalomyopathy. In vitro, the mutant proteins V142I, A185V, and R157stop have reduced activity on RNA-DNA hybrids. Analysis of patient samples show lower mtDNA levels and increased replication stalling. The disease causing mutations disrupt the conformational stability of RNase H1. RNase H1 mutations impair primer removal at OriL in vivo. The potential structural/functional consequences of the V142I and A185V mutations are assessed by looking at the crystal structure of wild-type RNase H1, PDB ID 2QK9. Both residues are located near the active site
malfunction
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RNase H2 and H1 knockout mutations in either of the human genes can cause Aicardi-Goutieres Syndrome, a severe inheritable neurodevelopmental disorder. In this disease, uncleaved RNA-DNA hybrids accumulate within cells that possibly upregulate interferon via the nucleic acid sensor cyclic GMP-AMP synthase (cGAS) and its adaptor protein STING
malfunction
strains with both flap endonuclease (Fen1) and RNase HII deleted grow well. GINS-associated nuclease, GAN, activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it is not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. Deletion of both Fen1 and GAN or of both RNase HII and GAN is lethal
malfunction
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DELTArnhA and DELTArnhC are synthetically lethal
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malfunction
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deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
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malfunction
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DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
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malfunction
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DELTArnhA and DELTArnhC are synthetically lethal
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malfunction
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deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
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malfunction
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DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
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metabolism
a two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL
metabolism
RNase H1 involvement in mtDNA synthesis, detailed overview. RNase H1 is involved in primer processing in human mitochondria
metabolism
the degradation of cleaved mRNA fragments by RNase H1-dependent ASOs involves XRN1, a cytoplasm-localized exonuclease, whereas the degradation of cleavage fragments of nuclear RNAs largely depend on XRN2, a nuclear-localized exonuclease
physiological function
ribonuclease H2 is the major nuclear enzyme involved in the degradation of RNA/DNA hybrids and removal of ribonucleotides misincorporated in genomic DNA
physiological function
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RNase H1 is an indispensable protein for Okazaki fragment processing in human mtDNA replication
physiological function
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RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutieres syndrome, a severe autoimmune disorder
physiological function
RNase H2 junction recognition is important for the removal of RNA embedded in DNA and may play an important role in DNA replication and repair
physiological function
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RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
physiological function
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both Pf-RNase HII and Pf-FEN-1 are required for the effective processing of an Okazaki substrate
physiological function
the enzyme is involved in RNA primer removal during DNA replication
physiological function
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ribonucleotide excision repair is most efficient when the ribonucleotide is incised by RNase H2. RNase H1 fails to substitute for RNase H2 in the incision step of ribonucleotide excision repair
physiological function
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RNase H is essential for foamy viral protease activity
physiological function
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RNase H2 is implicated in the processing of the 5' ends of Okazaki fragments. RNase H2 also links DNA replication and DNA repair through ribonucleotide excision repair. The RNase H2 interaction network also functions to suppress genome instability
physiological function
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RNase HI stimulates the activity of RnlA toxin
physiological function
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DNA replication requires RNA primers to initiate lagging strand DNA synthesis and their subsequent removal by the RNase. RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
R-loops are structures that form when RNA invades double-stranded DNA and hybridizes to complementary genomic sequences. R-loops can form spontaneously across many genomic loci, but the activity of two endogenous RNases H prevents their accumulation and persistence. RNase H enables efficient repair of R-loop induced DNA damage. RNase H1 and H2 are highly conserved ribonucleases with the ability to degrade the RNA moiety of a DNA:RNA hybrid. The RNases H are important protectors of genome stability, mechanisms, overview. The presence of either RNase H1 or H2 prevents the accumulation of DNA damage in G2-M
physiological function
ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function. Escherichia coli RNase H1 exhibits 3'-JRNase activity for dsDNAR1 much more effectively in the presence of manganese ions than in the presence of magnesium ions, regardless of whether this substrate is cleaved by 5'-JRNase activity of Escherichia coli RNase H2 in advance or not, and can excise the single ribonucleotide in collaboration with Escherichia coli RNase H2. Not only RNase H2 but also RNase H1 is involved in the RER pathway. Role of RNase H1 in DNA repair: removal of single ribonucleotide misincorporated into DNA in collaboration with RNase H2. The 3'-JRNase activity of Escherichia coli RNase H1 may not be involved in SOS response, because this activity may not be required for R-loop resolution
physiological function
Halalkalibacterium halodurans
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ribonucleotides within RNA-DNA hybrids are recognized and hydrolyzed by the RNase H enzymes
physiological function
RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
physiological function
RNase H1 is required for mtDNA replication, it directs origin-specific initiation of DNA replication in human mitochondria. RNase H1 is required for R-loop processing, primer formation, and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In addition to the potential role in R-loop processing, RNase H1 has also been proposed to be involved in mitochondrial pre-rRNA processing by interacting with the mitochondrial protein P32, which slightly enhances the RNase H1 enzymatic activity
physiological function
RNase H1-dependent antisense oligonucleotides (ASOs) can direct RNase H1 cleavage of target RNAs. ASOs are robustly active in directing RNA cleavage in both the cytoplasm and the nucleus. ASOs are effective in reducing the levels of targeted small nuclear RNAs (snRNAs), small cajal body RNAs (scaRNAs), small nucleolar RNAs (snoRNAs), and nucleoplasmic long non-coding RNAs (lncRNAs) and premRNAs. In the cytoplasm, RNase H1 is enriched in the mitochondria, where it is involved in mitochondrial DNA replication and RNA processing, by removing the RNA/DNA hybrids during replication and transcription. Pre-existing cytoplasmic mRNAs can be cleaved by RNase H1-ASO treatment. RNase H1-dependent ASOs reduce cytoplasmic mRNAs much faster than normal mRNA decay
physiological function
RNase H1-dependent antisense oligonucleotides (ASOs) can recruit RNase H1 to cleave the RNA substrate within the region complementary to the DNA portion of ASOs. ASOs can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs. Increasing the level of RNase H1 protein eliminates the enhancing effects of translation inhibition on ASO activity, suggesting that RNase H1 recruitment to ASO/mRNA heteroduplexes is a rate limiting step and that translating ribosomes can inhibit RNase H1 recruitment. Consistently, ASO activity is not increased by translation inhibition when targeting the 3' UTRs, independent of the translation efficiency of the mRNAs. Contrarily, the activity of 3' UTR-targeting ASOs tends to be reduced upon translation inhibition, likely due to decreased accessibility. Overexpression of RNaseH1 attenuates the enhancement in ASO activity by CHX treatment
physiological function
RNase HII is necessary for viability of Thermococcus kodakarensis. RNase HII is proposed to participate in primer processing during Okazaki fragment maturation. In Thermococcus kodakarensis, either flap endonuclease (Fen1) or GINS-associated nuclease (GAN) activity is sufficient for viability. GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN. Individually, Fen1, GAN, and RNase HII are not essential for viability
physiological function
RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
physiological function
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
physiological function
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the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The HBV reverse transcription mechanism features an initial endoribonucleolytic cut, 3'-5' degradation of RNA, and a sequence-independent terminal RNA cleavage
physiological function
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the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The RNaseH is one of two enzymatically active domains on the HBV polymerase that synthesizes the partially double-stranded DNA genome via reverse transcription. The reverse transcriptase (RT) domain of the polymerase protein copies the pregenomic RNA (pgRNA) template to form the minus-polarity DNA strand. The RNaseH recognizes RNA:DNA heteroduplexes that are formed during minus-polarity DNA synthesis and degrades the RNA strand. The polymerase then synthesizes the positive polarity DNA strand, but it typically arrests after making only about 50% of the plus-polarity DNA strand. Both enzymatic activities of the polymerase are required for synthesis of the HBV genome
physiological function
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the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
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the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life. R-loops are formed when an RNA strand intercalates into dsDNA, resulting in RNA-DNA hybrids and single-stranded DNA loops. R-loops affect promoter activities, with a role in gene expression (e.g. of the c-Myc proto-oncogene), genome stability, CRISPR-Cas immunity, DNA repair, and cancer formation. RNases H can remove the RNA moiety and prevent deleterious DNA breaks
physiological function
the role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key step in mitochondrial DNA maintenance. FEN1 or an enzyme with FEN1-like activity is required for the last step of L-strand maturation before ligation. RNase H1 alone is insufficient for maturation of the nascent L-strand during DNA synthesis, the FEN1-like activity together with RNase H1 is needed for efficient ligation at OriL. But FEN1 is not able to substitute for RNase H1 during primer removal and L-strand maturation
physiological function
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RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
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physiological function
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RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
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physiological function
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
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physiological function
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RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
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physiological function
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RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
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physiological function
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
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physiological function
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RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
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physiological function
Halalkalibacterium halodurans C-125
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ribonucleotides within RNA-DNA hybrids are recognized and hydrolyzed by the RNase H enzymes
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additional information
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RNase H exists as a free enzyme
additional information
the C-terminal RNase H domain loses the ability to suppress the RNase H deficiency of an Escherichia coli rnhA mutant, the hybrid binding domain is responsible for in vivo RNase H activity
additional information
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+. Residue Y163 is important for binding of both (5')RNA-DNA(3') junctions and RNA/DNA substrates
additional information
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the RNase HII contains a regulatory C-terminal tail. The C-terminus might form a short alpha-helix in which two residues, I195 and L196, are essential for the cleavage activity. The C-terminal alpha-helix is likely involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure. Structure and function of both archaeal RNase HII, overview
additional information
the RNASEH2A C-terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer
additional information
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the RNASEH2A C-terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer
additional information
the substrate binding site is located in the N-terminal TBP-like domain of RNase H3. The N-terminal domain of RNase H3 uses the flat surface of the b-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding
additional information
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the substrate binding site is located in the N-terminal TBP-like domain of RNase H3. The N-terminal domain of RNase H3 uses the flat surface of the b-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding
additional information
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the type 2 RNase H is an Mg2+- and alkaline pH-dependent enzyme
additional information
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translation initiates at each of the two in-frame AUGs of the Rnaseh1 mRNA, with the longer form being imported into mitochondria, regulation mechanisms, modelling, overview
additional information
Ala185 is adjacent to the catalytically essential Glu186, which coordinates a catalytic Mg2+ ion and forms part of a hydrophobic pocket that mediates the stabilising interactions in the active site region
additional information
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Ala185 is adjacent to the catalytically essential Glu186, which coordinates a catalytic Mg2+ ion and forms part of a hydrophobic pocket that mediates the stabilising interactions in the active site region
additional information
Halalkalibacterium halodurans
atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme, overview. The beta1 strand of the protein interacts with the DNA-RNA hybrid. Long timescale molecular dynamics simulations are performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers, analysis of recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation, overview. The active site region contains three aspartic acids (D10, D71 and D131) and two glutamic acids (E48 and E127) along with two Mg2+ ions and water molecules, active site dynamics. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove width seem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Key interactions located at the interface of enzyme-nucleic acid complex are responsible for its stability
additional information
Halalkalibacterium halodurans
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conformational changes induced by RNase H binding of RNA:DNA heteroduplexes, crystal structure analysis of a dodecameric nonpolypurine/polypyrimidine tract RNA-DNA duplex and of the same sequence bound to RNase H, overview. The structural changes to the duplex include widening of the major groove to 12.5 A from 4.2 A and decrease in the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H
additional information
enzyme EcRNH has an active site centered on a putative DDEED motif inxadstead of DEDD conserved in other species
additional information
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enzyme EcRNH has an active site centered on a putative DDEED motif inxadstead of DEDD conserved in other species
additional information
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the RNaseH active site contains four conserved carboxylates (the DEDD motif) that coordinate two divalent cations, usually Mg2+. The RNA cleavage mechanism requires both cations to promote a hydroxyl-mediated nucleophilic scission reaction
additional information
three-dimensional structure is solved, revealing a conserved protein architecture, the RNase H fold
additional information
Halalkalibacterium halodurans C-125
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conformational changes induced by RNase H binding of RNA:DNA heteroduplexes, crystal structure analysis of a dodecameric nonpolypurine/polypyrimidine tract RNA-DNA duplex and of the same sequence bound to RNase H, overview. The structural changes to the duplex include widening of the major groove to 12.5 A from 4.2 A and decrease in the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H
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