Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2₁2₁2

RNA-splicing endonuclease is responsible for the excision of introns in transfer RNA and archaeal ribosomal RNAs. The archaeal form of the enzyme recognizes a unique RNA motif that consists of two three-nucleotide bulges separated by a four base-paired helix, known as the bulge-helix-bulge (BHB) motif. A crystal structure of the RNA-splicing endonuclease from Archaeoglobus fulgidus (AF) has been reported previously at 2.8 Å. A truncated but fully active form of AF endonuclease that lacks the N-terminal domain was expressed and crystallized in an orthorhombic space group with two dimers in the asymmetric unit. The calculated native Patterson map suggests strong pseudo-face-centering characteristics, which lead to incorrect space-group assignment by the autoindexing program. The correct space group was determined to be P2₁2₁2 after reindexing. The structure was solved using molecular replacement and was refined to 2.0 Å. The truncated AF endonuclease structure is essentially identical to the corresponding portion of the wild-type AF endonuclease structure in space group P4₃2₁2 as reported previously, with the exception of loop L9, which differs owing to different crystallographic packing. These results confirm the previously described structural features of dimeric splicing endonuclease.