CULT domain sequence and structure.

<p>(<b>a</b>) Multiple alignment of CULT domains from representative members of the groups in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi-1004023-g002" target="_blank">Fig. 2</a>. The alignment is based on the results of the PSI-Blast search with the CULT domain of human cereblon (first sequence in the alignment). Invariant residues of the three core groups (cereblon, secreted eukaryotic, bacterial) are underscored in black, residues conserved in at least two thirds of the sequences in the alignment are highlighted in dark grey and residues in at least one third of the sequences in light grey. The three tryptophan residues forming the thalidomide-binding site are marked by arrowheads and the two cysteine motifs coordinating the Zn ion, as well as a highly conserved motif at the tip of the inserted β-hairpin, are written out. The secondary structure above the alignment (S = β-strand) is the experimentally determined structure of the CULT domain from MGR_0879 of <i>Magnetospirillum gryphiswaldense</i> (first bacterial sequence in the alignment; <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023-Hartmann1" target="_blank">[18]</a>). The β-strands of the two main β-sheets are numbered according to the consensus structure of the β-tent fold and colored by whether they belong to the N-terminal β-sheet (purple) or the C-terminal one (gold); β3 is shown in brackets as it has lost its β-strand character in the CULT domain. The two β-strands of the inserted hairpin (teal) are labeled βI1 and βI2. The sequences are: (cereblon) HS - <i>Homo sapiens</i> NP_057386.2, DR - <i>Danio rerio</i> NP_001003996.1, DM - <i>Drosophila mojavensis</i> XP_001999319.1, CE - <i>Caenorhabditis elegans</i> NP_502300.2, AT - <i>Arabidopsis thaliana</i> NP_850069.1, EH - <i>Entamoeba hystolitica</i> XP_657530.1; (secreted eukaryotic) DR - <i>Danio rerio</i> NP_001121712.1, CB - <i>Caenorhabditis brenneri</i> EGT59438.1, TA - <i>Trichoplax adhaerens</i> XP_002115135.1, NV - <i>Nasonia virtipennis</i> XP_003427162.1; (bacterial) MG - <i>Magnetospirillum gryphiswaldense</i> CAM74667.1, GP - gamma proteobacterium BDW918 WP_008249149.1, HO - <i>Haliangium ochraceum</i> WP_012831591.1, DT - <i>Desulfonatronospira thiodismutans</i> WP_008870657.1, LS - <i>Leptospira</i> sp. B5-022 WP_020769190.1; (oomycete) PI - <i>Phytophthora infestans</i> XP_002999235.1, AL - <i>Albugo laibachii</i> CCA16326.1; (kinetoplastid) LM - <i>Leishmania major</i> strain Friedlin XP_001681231.1, TC - <i>Trypanosoma cruzi</i> EKG02463.1; (other) BP - <i>Bathycoccus prasinos</i> XP_007508760.1. (<b>b</b>) Superimposition of bacterial and eukaryotic CULT domain structures from <i>M. gryphiswaldense</i> (red), <i>H. sapiens</i> (blue; PDB ID:4TZ4), <i>M. musculus</i> (orange; PDB ID: 4TZC), and <i>G. gallus</i> (green; PDB ID:4CI2). The r.m.s. deviations in Cα positions for the pairwise comparisons ranged between 0.4 and 0.9 Å and are listed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023.s004" target="_blank">S1 Table</a>. (<b>c</b>) Superimposition of the thalidomide binding site for the structures in panel (b). The ligand and the residues of the aromatic cage are shown in stick representation and colored as in panel (b). Residue numbering is for the human protein.