Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif

• Crystal structure of metagenome-derived LC9-RNase H1 was determined.
• The LC9-RNase H1 structure highly resembles the E. coli RNase H1 structure.
• LC9-RNase H1 has an atypical DEDN active site motif.
• LC9-RNase H1 homologues are evolutionarily distantly related to other RNases H1.

The crystal structure of metagenome-derived LC9-RNase H1 was determined. The structure-based mutational analyses indicated that the active site motif of LC9-RNase H1 is altered from DEDD to DEDN. In this motif, the location of the second glutamate residue is moved from αA-helix to β1-strand immediately next to the first aspartate residue, as in the active site of RNase H2. However, the structure and enzymatic properties of LC9-RNase H1 highly resemble those of RNase H1, instead of RNase H2. We propose that LC9-RNase H1 represents bacterial RNases H1 with an atypical DEDN active site motif, which are evolutionarily distinct from those with a typical DEDD active site motif.