Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
Fig 8
(A) Distribution of ligands from “Nucleotide/nucleoside” superclass for H-groups with more than 10 EC reactions. KEGG compounds (colored and classified according to classes of “Nucleotide/nucleoside” superclass in legend) by assigned fraction of EC reactions in particular homology groups (Y-axis) are distributed across ECOD H-groups with more than 10 unique EC numbers (X-axis). Values in parenthesis show the number of unique EC numbers per H-group. (B-E) 5’-deoxyribonucleosides reveal different binding modes in different H-groups. RLM (SSEs colored rainbow, with yellow crossover loop) bind adenine nucleotide (magenta stick) of SAH/MTA. 5’-deoxyribonucleosides-binding Rossmann-fold domain (slate cartoon) from (B) Mouse nicotinamide N-methyltransferase (PDB: 2I62, EC: 2.1.1.1) binds SAH, the Asp/Glu motif is shown by the red sphere (C) methyltransferase (PDB: 2CX8, EC: 2.1.1.193) binds SAH, the “knot” is formed by the blue β-strand, magenta loop, cyan α-helix and red β-strand with the following loop, which is located under the magenta loop, (D) MTA/AdoHcy nucleosidase (PDB: 1Z5O, EC: 3.2.2.9) binds 5'-methylthioadenosine (MTA), (E) 5'-fluoro-5'-deoxyadenosine synthase (PDB: 1RQP, EC: 2.5.1.63) binds SAM.