Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation

Xu et al. 10.1073/pnas.0600443103.

Supporting Information

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Supporting Figure 4
Supporting Figure 5
Supporting Figure 6
Supporting Table 1
Supporting Figure 7
Supporting Table 2
Supporting Table 3
Supporting Table 4

Supporting Figure 4

Fig. 4. Sequence alignment of yeast (Bottom), Escherichia coli, Salmonella typhimurium, Thermotoga maritima, Lactobacillus leichmannii, Mus musculus, and Homo sapiens Rnr1s. The structures of yeast, E. coli, S. typhimurium, and L. leichmannii were structurally aligned. The conserved cysteines in the active site and the C-terminal tail are highlighted in yellow. Sequences highlighted in gray are areas that are disordered or do not appear in the PDB files and, therefore, cannot be structurally aligned. The catalytic asparagine and glutamate are highlighted in black, and the loop 1 and loop 2 regions are highlighted in green and purple, respectively. Red and blue highlights represent a -helix and b -sheet. The cyan stars in the L. leichmannii sequence represent a 124-residue stretch containing loop 1, shown at the bottom of the sequence. No structure exists for M. musculus or H. sapiens Rnr1, and their alignments are based solely on sequence similarity to Saccharomyces cerevisiae. Numbering across the top and bottom rows represents amino acid number in E. coli and S. cerevisiae.

Supporting Figure 5

Fig. 5. Structure of yeast Rnr1. Stereo figure of apo Rnr1, with effector and substrate from the dGTP–ADP structure modeled in to show the specificity and catalytic sites; the three-helix insert (THI) and C-terminal insert (CI) are colored red and blue, respectively.

Supporting Figure 6

Fig. 6. Topology diagram of Rnr1, showing b -strands as arrows and a -helices as cylinders. Inserted parts are colored as in Fig. 5. Additional inserts not shown in that figure are colored green.

Supporting Figure 7

Fig. 7. Conservation of the floor of the effector-binding site. The thymin triphosphate (TTP) specificity effector and the aliphatic floor of the specificity site are shown for yeast TTP–GDP-bound Rnr1 (blue), S. typhimurium TTP-bound Rnr1 (yellow) and for E. coli TTP–GDP-bound Rnr1 (gray). Yeast residues are labeled in blue; dot surfaces are shown for aliphatic residues in the floor of the specificity site. Helices A and B (and A' and B' from the other monomer) are labeled in black. Note the orthogonal phenylalanine from helix B of E. coli that substitutes for Y285 of helix B' for yeast.