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. 2018 Mar 19;115(14):E3211–E3220. doi: 10.1073/pnas.1720871115

Fig. 2.

Fig. 2.

Structural characteristics of CDA1-like proteins. (A) Sequence alignment of Homo sapiens AID (HsAID), Mus musculus AID (MmAID), Danio rerio AID (DrAID), Petromyzon marinus CDA1 (PmCDA1), Lampetra planeri CDA1 (LpCDA1), L. japonica CDA1 (LjCDA1), L. planeri (Lp), and L. japonica (Lj) LpCDA1L1 proteins. The secondary structure of HsAID was used to denote α-helical (α), β-strand (β), and secondary catalytic loop (L) regions. The conserved Zn-coordinating residues (cysteines, histidine, and glutamic acid) are denoted by asterisks. Conserved secondary catalytic residues are indicated by diamonds; note that the replacement of threonine 27 by cysteine in PmCDA1 (and by inference in LpCDA1 and LjCDA1) does not impair enzymatic activity (25) (Fig. 3). Positively and negatively charged residues are colored blue and red, respectively. (B) Summary table indicating the predicted chemical properties of human AID and L. planeri CDA1L1 proteins. (C) Representative surface topology models of the lamprey CDA1L1 proteins, compared with P. marinus CDA1 (PmCDA1), zebrafish AID (DrAID), mouse AID (MmAID), and human AID (HsAID), respectively. Positively and negatively charged residues are colored blue and red, respectively. The catalytic pockets are indicated as an indentation in the center, with the Zn-coordinating triad of two cysteines and a histidine, as well as the catalytic glutamic acid colored purple. The net charge differed among the LpCDA1L1 genes such that LpCDA1L_1– 3 were net-negatively charged, while LpCDA1L1_4 was net-positively charged, akin to PmCDA1, DrAID, MmAID, and HsAID. Regardless of net charge, a concentration of positively charged residues near the catalytic pocket in all LpCDA1L1 proteins is notable. (D) Models of the catalytic pockets of LpCDA1L1_4 and human AID (HsAID) docked with (d)C in a deamination-feasible configuration, showing the interactions between the Zn-coordinating triad and target (d)C; the coordinated Zn is depicted as a gray sphere, with the Zn-coordinating and catalytic glutamic acid residues colored purple.