Fig. 3: Comparison of mitochondrial GTPBP10, GTPBP5, and bacterial ObgE.
From: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome
a–c A comparison of the mitochondrial ObgE homologs GTPBP10 and GTPBP5 with its bacterial counterpart is shown. For comparison the ribosomal RNA of the large subunit from intermediate 1, PDB 7ODT (GTPBP5), and PDB 7BL2 (ObgE) has been superimposed and conserved ribosomal elements are highlighted in the images. It is apparent that the proteins diverge in the length of their Obg domain loops 1 and 3, which have been labeled with numbers in the images. SRL = sarcin-ricin loop, PTC = peptidyl transferase center (d) Superposition of the Obg domain of GTPBP5 (PDB 7ODT) onto the Obg domain of GTPBP10 shows that GTPBP5 is sterically incompatible with GTPBP7 in intermediate 1. e Overview of the location of the GTPase domain and the bound nucleotide in the context of ribosomal RNA helix H89, the ribosomal stalk base containing uL11m, the sarcin-ricin loop (SRL), and biogenesis factor MALSU1. Switch II containing the catalytic Walker B motif (DxxG) is colored in cyan highlighted. The region detailed in (g) is boxed. f, g Contact sites between GTPBP10 and MALSU1 as well as the bacterial ObgE with RsfS (PDB 7BL2) are shown. The sharpened, supersampled EM density for intermediate 1 is displayed as semi-transparent surface. The loop likely aids to anchor the GTPBP10 GTPase domain via MALSU1 on SRL as it was one of the best-resolved regions within the GTPase domain.
