Abstract of the PDB Structure's related Publication:
The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.
The multi-site specific RluC catalyzes isomerization of uridines to pseudouridines at positions 955 (in hairpin 39 of Domain II), 2504 (in single stranded region between hairpins 89-90 of Domain V in Peptidyl Transferase Center) and 2580 (in stem of helix 90 of the same Domain V) in 23S rRNA. In vitro transcript of 23S ribosomal RNA was used as substrate. RluC possess a N-terminal S4 RNA binding domain. Proteolytically derived fragment of the enzyme consisting of residues 89-319 has been crystallized and shown to retain catalytic activity. RluC belongs to the same subgroup of RNA pseudourodine synthases as RluA, RluD, TruC, Pus5, Pus6, Pus8 and Pus9.