![]() Bh-RNase H has two Mg2+ ions per subunit - four total ions for the homodimer-that facilitate the nucleophilic attack (1). The hydrolysis of the phosphodiester bond is driven by nucleophilic attack from a hydroxyl group that forms from a deprotonated water molecule (2). RNase H catalyzes the RNA hydrolysis by positioning the nucleotides, the metal-ion ligands (Mg 2+ or Mn2+), and the nucleophile all within the active site. RNase H bound to an RNA/DNA hybrid in Bacillus halodurans is a homo-dimer that consists of two identical polypeptide chains surrounding a nucleotide substrate with one DNA strand and one RNA strand. Thus, hydrolysis yields products with 5’phosphate and 3’ hydroxyl termini (3). The hydrolysis occurs at the oxygen of the 3’ carbon in one nucleotide and the phosphate of the 5’ carbon of the adjacent nucleotide, regardless of the specific nucleotide base sequence. ![]() RNA degradation occurs through sequence-nonspecific hydrolysis of the P-O3’ bond in the RNA backbone (2). However, RNase H also plays an important role in retroviruses like HIV by destroying the RNA template after the cDNA strand has been created in reverse transcription-a process that allows the virus to replicate (1). RNase H removes RNA primers from Okazaki fragments during DNA replication in cells like those of Bacillus halodurans (Bh). ![]() Ribonuclease H (RNase H) mutant D132N (PDB ID: 1ZBI) is an endonuclease that degrades RNA from a RNA/DNA hybrid. RNase H mutant D132N (1ZBI) from Bacillus halodurans ![]()
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