Crystal structure of an RtcB homolog protein (PH1602‐extein protein) from Pyrococcus horikoshii reveals a novel fold

The hypothetical extein, PH1602-extein (53.5 kDa, 481 residues) from the hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3, shows sequence similarity to Escherichia coli RtcB (33% identity). RtcB homologs are conserved in all archaebacteria, in most eukaryotes, including metazoa, and in a wide variety of eubacteria.In E. coli, the rtcB gene, together with rtcA and rtcR, comprise the 54-dependent operon termed the RNA 3-terminal phosphate cyclase operon. The functions of the gene products RtcA and RtcR have been characterized previously as RNA 3-terminal phosphate cyclase and 54-specific regulator, respectively. On the other hand, although RtcB is highly conserved among many organisms, there have been few studies of RtcB and its homologs.In a previous study, it was suggested that human RtcB homolog may form a heterotrimer with DDX1 (putative RNA helicase) and CGI-99 (ninein-interaction protein). These three proteins were pulled down by double-stranded DNA fragments. The artificial DNA sequences included an 11-bp inverted repeat, thus enabling formation of a cruciform structure. The manner of interaction between the presumptive trimer and double-stranded DNA has not been clarified.Sequence analysis indicated that the ph1602 gene encodes an RtcB homolog with an intervening intein. Thus, translation products of ph1602 are considered to generate two mature proteins, PH1602-intein and PH1602-extein, because of the protein-splicing activity of the intein. We cloned the extein sequence of PH1602 and successfully overexpressed, purified, and crystallized the PH1602-extein. Here, we report the crystal structure of PH1602-extein at 2.15 Å resolution, determined by the single-wavelength anomalous diffraction (SAD) method