Volume 100, Issue 3, Pages 311-321 (February 2000) The Crystal Structure of Human Eukaryotic Release Factor eRF1—Mechanism of Stop Codon Recognition and Peptidyl-tRNA Hydrolysis  Haiwei Song, Pierre Mugnier, Amit K Das, Helen M Webb, David R Evans, Mick F Tuite, Brian A Hemmings, David Barford  Cell  Volume 100, Issue 3, Pages 311-321 (February 2000) DOI: 10.1016/S0092-8674(00)80667-4

Figure 1 Orthogonal Views of eRF1 The figure indicates the position of the GGQ sequence motif at the tip of domain 2 and the suppressor mutant Arg-68 on the α-2/α-3 helix hairpin of domain 1. Figure produced by MOLSCRIPT (Kraulis 1991) and RASTER3D (Merit and Murphy 1994). Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 2 Multiple Sequence Alignment of Class 1 Release Factors Human eRF1, S. cerevisiae eRF1 (SUP45), and Archaea (Pyrococcus abyssi) RF1 were aligned using MULTALIGN (Barton 1990). Invariant residues are colored red. The GGQ motif is denoted with blue arrows, and the corresponding E. coli RF1 sequence is aligned below. Secondary structure elements are indicated. Figure drawn using ALSCRIPT (Barton 1993). Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 3 Amino Acid Changes in the GGQ Motif Lead to Nonfunctional eRF1 In Vivo in Yeast Haploid strain ΔLE2[pUKC803] in which the chromosomal sup45::HIS3 disruption is complemented by a URA3 plasmid encoding SUP45 was transformed with mutated derivatives of pUKC1901 and subsequently grown on either YEPD media (A) or Minimal Medium containing 5FOA (B and C). The plasmid, pRS315, which lacks SUP45, was used as the control. (A) Four derivatives of this plasmid were tested that encode modified eRF1 where GGQ has been modified as AGQ, GAQ, AAQ, or GGL, respectively. None of the mutants tested were dominant lethal at 30°C. The double mutant G180A-G181A generated an Ade+ white phenotype. (B) After loss of the URA3 plasmid, none of the mutants could support viability when compared to the wild-type-eRF1. Identical results were obtained for the Q182R and Q182L mutants (data not shown). (C) The G180A, G181A, and G180A-G181A double mutants display dominant-negative phenotypes, conferring adenine prototrophy on the strain. Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 4 Detailed View of the GGQ Minidomain (A) Stereo view of residues Pro-177 to Leu-193. The view is rotated 180° relative to Figure 1A. (B) Solvent accessible surface and electrostatic potential of eRF1 viewed as in Figure 1A. The figure reveals the positive electrostatic potential of the GGQ minidomain. Arg and Lys residues of the GGQ minidomain are labeled. Figure produced using GRASP (Nicholls et al. 1991). Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 5 Schematic of the Reactions Catalyzed at Peptidyl Transferase Center of the Ribosome (A) Transesterification reaction. (B) Proposed scheme for hydrolysis of the peptidyl-tRNA bond in site P by a catalytic water molecule coordinated by Gln-185 of the eRF1 GGQ motif in site A. Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 6 Molecular Mimicry of tRNA Molecules Ribbon diagram of eRF1 and yeast tRNAPhe structures, revealing similar shapes and overall dimensions. The disposition of domains 1, 2, and 3 of eRF1 matches those of the tRNA anticodon loop, aminoacyl stem, and T stem, respectively. The site of attachment of an aminoacyl group at the CCA stem is indicated. Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)

Figure 7 Molecular Surface Views of eRF1 and Yeast tRNAPhe (A) Molecular surface of eRF1 revealing regions of high to low sequence conservation between eukaryotic eRF1 and Archaea RF sequences, corresponding to a color ramp from red to blue, respectively. The figure depicts the conserved groove present on domain 1, and invariant residues including the NIKS motif (residues 62–65) are labeled. The molecule is rotated 90° relative to the view in Figure 1A and Figure 4B. (B) View of yeast tRNAphe showing the relative disposition of the anticodon bases and the amino group of an aminoacyl residue attached to the CCA stem. The distance between these sites matches the distance between the conserved groove on domain 1 of eRF1 and Gln-185 of the GGQ motif. Cell 2000 100, 311-321DOI: (10.1016/S0092-8674(00)80667-4)