Ribonuclease H

ribonuclease H
Crystallographic structure of E. coli RNase HI.
Identifiers
EC number	3.1.26.4
CAS number	Template:CAS
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / EGO
Search PMC articles PubMed articles NCBI proteins

retroviral ribonuclease H
Identifiers
EC number	3.1.26.13
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Search PMC articles PubMed articles NCBI proteins

Ribonuclease H (RNase H) is a family of non-sequence-specific endonucleases that catalyze the cleavage of RNA via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes.

RNase H’s ribonuclease activity cleaves the 3’-O-P bond of RNA in a DNA/RNA duplex substrate to produce 3’-hydroxyl and 5‘-phosphate terminated products. In DNA replication, RNase H is responsible for removing the RNA primer, allowing completion of the newly synthesized DNA.

Structure

The 3-D structure of RNase H commonly consists of a 5-stranded β-sheet surrounded by a distribution of α-helices. In some RNase H, such as the one found in HIV-1, the enzyme is missing one of the helices known as the C-helix, a positively charged α-helix whose protrusive shape increases substrate binding capacity. The active site of the enzyme is centered around a conserved DEDD motif (composed of residues: D443, E478, D498, and D549) which performs the hydrolysis of the RNA substrate. A magnesium ion is commonly used as a cofactor during the hydrolysis step. It is also a potential but unconfirmed mechanism in which multiple ions are necessary to perform the hydrolysis. The enzyme also contains a nucleic acid binding cleft about 60 Å in length that can encompass a region of 18 bound RNA/DNA base pairs.

Function

Because RNase H specifically degrades only the RNA in RNA:DNA hybrids, it is commonly used in molecular biology to destroy the RNA template after first-strand complementary DNA (cDNA) synthesis by reverse transcription, as well as in procedures such as nuclease protection assays. RNase H can also be used to degrade specific RNA strands when the cDNA oligonucleotide is hybridized, such as the removal of the polyadenine tail from mRNA hybridized to oligo(dT), or the destruction of a chosen non-coding RNA inside or outside the living cell. To terminate the reaction, a chelator, such as EDTA, is often added to sequester the required metal ions in the reaction mixture.

Mechanism

Proposed HIV-1 RNase H mechanism

Genes

The following human genes encode proteins with RNase H activity:

• ERVK6
• RNASEH1
• RNASEH2A
• RNASEH2B
• RNASEH2C

Role in Disease

Mutations in the RNASE2 genes are associated with the rare human genetic disorder known as Aicardi–Goutieres syndrome, which manifests as neurological and dermatological symptoms at an early age.

Retroviral RNase H, a part of the viral reverse transcriptase enzyme, is an important pharmaceutical target, as it is absolutely necessary for the proliferation of retroviruses, such as HIV and murine leukemia virus. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. While not an effective treatment option, incorporation of 6-deoxythioguanosine has been shown to inhibit RNase H cleavage of the DNA/RNA complex.

HIV-1

Within human immunodeficiency virus type 1 (HIV-1), RNase H exists as a domain in the heterodimeric HIV-1 reverse transcriptase enzyme. HIV-1 carries out reverse transcription, a process that produces new double-stranded DNA from the viral genome's single-stranded RNA. During DNA synthesis, a DNA/RNA hybrid is formed as a replication intermediate and must be cleaved by RNase H before the process can continue. RNase H performs three types of cleaving actions: non-specific degradation of the (+)-strand RNA genome, specific removal of the (-)-strand tRNA primer, and removal of the (+)-strand purine-rich polypurine tract (PPT) primer. RNase H plays a role in the priming of the (+)-strand, but not in the conventional method of synthesizing a new primer sequence. Rather RNase H creates a "primer" from the PPT that is resistant to RNase H cleavage. By removing all bases but the PPT, the PPT is used as a marker for the end of the U3 region of its long terminal repeat.

Applications

DNA Amplification

IDT introduced a method - RNase H-dependent PCR (rhPCR) - to increase specificity on polymerase chain reaction by using RNase H2, where it has low activity at room temperature and optimal activity around 70°C to act as hot start PCR feature, from Pyrococcus abyssi and the blocked primers the contain a single ribonucleotide residue. PCR on target amplification can start only when the single ribonucleotide residue in the primers with complementary binding to the target DNA lead to its cleavage for primer activation.

Nucleic acid identification

Nucleic acid identification can be achieved by the recognition and binding of target DNA by the designated RNA probe. The enzyme RNase H can selectively and repeatedly destroy only RNA probe from DNA−RNA duplexes for signal amplification to detection limit of femtomole level. Sensing technology surface plasmon resonance was used to monitor the specific cleavage of RNA probe for microRNA profiling in influenza diagnosis.

External links

• GeneReviews/NCBI/NIH/UW entry on Aicardi-Goutières Syndrome
• RNase H at the US National Library of Medicine Medical Subject Headings (MeSH)