Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes

@article{Tadokoro2009RibonucleaseHM,
  title={Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes},
  author={Takashi Tadokoro and Shigenori Kanaya},
  journal={The FEBS Journal},
  year={2009},
  volume={276}
}
The prokaryotic genomes, for which complete nucleotide sequences are available, always contain at least one RNase H gene, indicating that RNase H is ubiquitous in all prokaryotic cells. Coupled with its unique substrate specificity, the enzyme has been expected to play crucial roles in the biochemical processes associated with DNA replication, gene expression and DNA repair. The physiological role of prokaryotic RNases H, especially of type 1 RNases H, has been extensively studied using… 
View on Wiley
ncbi.nlm.nih.gov
171 Citations
Highly Influential Citations
14
Background Citations
64
Methods Citations
8

171 Citations

Citation Type

Citation Type

Ribonuclease H: the enzymes in eukaryotes
TLDR
Some of the most recent findings on eukaryotic RNases’H1 and H2 are discussed, focusing on the structural data on complexes between human RNase’h1 and RNA/DNA hybrids that had provided great detail of how the hybrid binding‐ andRNase H‐domains recognize and cleave the RNA strand of the hybrid substrates.
RNases H: Structure and mechanism.
Structure and Function of RNase H Enzymes
TLDR
RNase H enzymes are endonucleases that specifically cleave ribonucleotides within an RNA:DNA duplex, and at least one type of RNase H is found in most organisms.
Characterization of a new RNase HII and its essential amino acid residues in the archaeon Sulfolobus tokodaii reveals a regulatory C-terminus
TLDR
The data suggest that the C-terminal α-helix is likely involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure, and offer important clues for further understanding the structure and function of both archaeal and eukaryotic RNase HII.
Bacterial ribonucleases and their roles in RNA metabolism
TLDR
A detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of the current knowledge has been derived.
Structure-Specific Nuclease Activities of Pyrococcus abyssi RNase HII
TLDR
PabRNase HII was revealed as a dual-function enzyme likely required for the completion of DNA replication and DNA repair and introduction of mismatches into the RNA portion near the RNA-DNA junction decreased both the specificity and the efficiency of cleavage.
Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site
TLDR
Molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states suggest that the active site is highly rigid in the apo state of all homologys studied and is conformationally preorganized to favor the binding of a magnesium ion.
The Structural and Biochemical Characterization of Human RNase H2 Complex Reveals the Molecular Basis for Substrate Recognition and Aicardi-Goutières Syndrome Defects*
TLDR
The crystal structure of the Thermotoga maritima RNase H2-substrate complex is modeled and the model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition.
Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site
TLDR
Molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states suggest that the active site is highly rigid in the apo state of all homologys studied and is conformationally preorganized to favor the binding of a magnesium ion.
Structure-specific nuclease activities in Pyrococcus abyssi RNase HII 1 2
TLDR
PabRNase HII was revealed as a dual-function enzyme likely required for completion of DNA replication and DNA repair and introduction of mismatches in the RNA portion near the RNA-DNA junction decreased both specificity and efficiency of cleavage by PabRNA HII.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 73 REFERENCES
Molecular diversities of RNases H.
Crystal structure of archaeal RNase HII: a homologue of human major RNase H.
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7.
TLDR
Similarities in primary structure and biochemical characteristics between S.tokodaii RNase HI and reverse transcriptases imply that the S.kodaii enzyme might be derived from the RNase H domain of reverse transcriptase.
Heat labile ribonuclease HI from a psychrotrophic bacterium: gene cloning, characterization and site-directed mutagenesis.
TLDR
Site-directed mutagenesis studies suggest that the amino acid substitution in the middle of the alphaI-helix partly accounts for the difference in the stability and activity between SIB1 and E.coli RNases HI.
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X‐ray crystallographic and mutational analyses
TLDR
The catalytic center of an archaeal Type 2RNase H has been identified by a combination of X‐ray crystallographic and mutational analyses, and the structure suggests that the C‐terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.
Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication.
TLDR
Structural and mutational results together suggest a molecular mechanism for type 2 RNase H enzymes for the specific recognition and cleavage of RNA in the RNA-DNA junction within hybrid duplexes, which reconciles the broad substrate binding affinity with the catalytic specificity observed in biochemical assays.
Crystal structure of type 1 ribonuclease H from hyperthermophilic archaeon Sulfolobus tokodaii: role of arginine 118 and C-terminal anchoring.
TLDR
Differential scanning calorimetry measurements indicated that Sto-RNase HI is a hyperstable protein with a melting temperature of 102 degrees C, and mutations of the cysteine residues forming disulfide bond or elimination of the extreme C-terminal region greatly destabilized the protein, indicating that anchoring of the C-Terminal tail is responsible for hyperstabilization of Sto- RNase HI.
Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.
TLDR
Site-directed mutagenesis studies suggest that the difference in the number of intramolecular ion pairs partly accounts for the differences in stability between MR-1 and E. coli RNases HI.
Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes
TLDR
This is the first empirical study to show the effect of functional redundancy on changes in gene constitution during the course of evolution and provide two possible evolutionary models for RNase H genes in which functional redundancy contributes to the exclusion of redundant genes from the genome of a species.
...
1
2
3
4
5
...