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 for 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.
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