Volume 20, Issue 6, Pages 917-927 (December 2005) Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC  Marc Graille, Valérie Heurgué-Hamard, Stéphanie Champ, Liliana Mora, Nathalie Scrima, Nathalie Ulryck, Herman van Tilbeurgh, Richard H. Buckingham  Molecular Cell  Volume 20, Issue 6, Pages 917-927 (December 2005) DOI: 10.1016/j.molcel.2005.10.025 Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 1 Ribbon Representation of the PrmC-RF1 Complex (A) and Detailed View of the PrmC Active Site (B) (A) The PrmC Nter and Cter domains and the linker connecting these two domains are shown in green, blue, and cyan, and the RF1 domains 1, 2, 3, and 4 are colored yellow, pink, orange, and red, respectively. AdoHCy and the RF1 residue Gln 235 side chain are shown as sticks. The AdoHCy sulfur atom is colored green. The GGQ motif and the PAT anticodon loop from RF1 are in gray and green, respectively. (B) Stereo view representation of RF1 Gln 235 interactions with PrmC. The Cα traces of PrmC Nter, linker, and Cter domains and RF1 domain 3 are shown in green, blue, gray, and orange, respectively. The PrmC side chain residues and AdoHCy are colored in blue and yellow, respectively. RF1 Gln 235 is in orange. The AdoMet methyl group to be transferred to Gln 235 is modeled by a gray sphere. Hydrogen bonds are indicated by red dashed lines. The distance between the Gln 235 Nε2 atom and the AdoMet methyl group is shown as black dashed lines. The 2Fo-Fc electron density contoured at 1σ is depicted around the AdoHCy cofactor, and the RF1 Gln 235 side chain is shown in violet. Molecular Cell 2005 20, 917-927DOI: (10.1016/j.molcel.2005.10.025) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 2 Sequence Alignment of Prokaryotic Class I Release Factors Strictly conserved residues are in white on a black background. Partially conserved amino acids are boxed. Residues conserved in most of the members of one family, but not conserved in the other one, are on a gray background. The EcRF1 positions involved in PrmC binding are indicated by filled circles under the sequence. Domain limits are indicated above the sequence. Figures 2 and 3 were made with the ESPript server (Gouet et al., 1999). Molecular Cell 2005 20, 917-927DOI: (10.1016/j.molcel.2005.10.025) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 3 Sequence Alignment of Bacterial PrmC Methyltransferases Strictly conserved residues are in white on a black background. Partially conserved amino acids are boxed. PrmC positions involved in RF1 binding are indicated by filled circles under the sequence. Molecular Cell 2005 20, 917-927DOI: (10.1016/j.molcel.2005.10.025) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 4 Detailed View of PrmC Nter Domain Interactions with RF1 Domain 2 and Release Factors Conformational Changes (A) Close-up of main PrmC (green) and RF1 (violet) residues involved at the PrmC Nter domain-RF1 domain 2 interface. The salt bridges made between PrmC Glu 44 and RF1 Arg 133 and 137 are depicted by black dashed lines. (B) Superpositions of PrmC structures. The unbound EcPrmC (green) and Gln bound TmPrmC (magenta) structures have been fitted onto the RF1 bound EcPrmC (yellow). The superposition has been done on the AdoMet binding domain. The AdoHCy ligand is shown as sticks. (C) Comparison of the conformations of E. coli RF as described by X-ray (left panel, PrmC bound RF1, this study) or electron cryo-microscopy (right panel, ribosome bound RF2, Klaholz et al., 2003; Rawat et al., 2003). Domain 3 (orange) is shown in the same orientation for both panels. The same color code as in Figure 1A is used to identify RF domains. The GGQ motif and the anticodon loop are represented as sticks. Molecular Cell 2005 20, 917-927DOI: (10.1016/j.molcel.2005.10.025) Copyright © 2005 Elsevier Inc. Terms and Conditions