The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold
Figure 3
CULT domain sequence and structure.
(a) Multiple alignment of CULT domains from representative members of the groups in Fig. 2. 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 Magnetospirillum gryphiswaldense (first bacterial sequence in the alignment; [18]). 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 - Homo sapiens NP_057386.2, DR - Danio rerio NP_001003996.1, DM - Drosophila mojavensis XP_001999319.1, CE - Caenorhabditis elegans NP_502300.2, AT - Arabidopsis thaliana NP_850069.1, EH - Entamoeba hystolitica XP_657530.1; (secreted eukaryotic) DR - Danio rerio NP_001121712.1, CB - Caenorhabditis brenneri EGT59438.1, TA - Trichoplax adhaerens XP_002115135.1, NV - Nasonia virtipennis XP_003427162.1; (bacterial) MG - Magnetospirillum gryphiswaldense CAM74667.1, GP - gamma proteobacterium BDW918 WP_008249149.1, HO - Haliangium ochraceum WP_012831591.1, DT - Desulfonatronospira thiodismutans WP_008870657.1, LS - Leptospira sp. B5-022 WP_020769190.1; (oomycete) PI - Phytophthora infestans XP_002999235.1, AL - Albugo laibachii CCA16326.1; (kinetoplastid) LM - Leishmania major strain Friedlin XP_001681231.1, TC - Trypanosoma cruzi EKG02463.1; (other) BP - Bathycoccus prasinos XP_007508760.1. (b) Superimposition of bacterial and eukaryotic CULT domain structures from M. gryphiswaldense (red), H. sapiens (blue; PDB ID:4TZ4), M. musculus (orange; PDB ID: 4TZC), and G. gallus (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 S1 Table. (c) 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.