From: Natural history of S-adenosylmethionine-binding proteins
Reaction summary | Trivial name, EC number | Sequence families and spatial folds (summary) | Evolutionary roots and status in LUCA |
---|---|---|---|
Methyl transfer | SAM-dependent methyltransferase, EC:2.1.1.- | Five classes: I, Rossmann fold; II, reactivation domain of methionine synthase; III, "corrinoid-like" MTases; IV, SPOUT domain; V, SET domain. Classes I-IV are α/β folds, class V is a β-clip. The Rossmann-fold MTases are the largest class of SAM-dependent enzymes. The folds of Classes II and III are unique. Trm10 and TrmH families of RNA MTases appear to be the modified versions, of, respectively, class IV fold [47], [49] and class I fold fused to PP-superfamily ATPase (this study). GTP MTase of Sindbis-like viruses may belong to α/β class, but specific fold prediction is unavailable | Several distinct Rossmann-fold methyl transferases in LUCA. |
Methylene transfer | Cyclopropane fatty acid synthase, EC:2.1.1.79 | Rossmann-fold methyltransferase family | Derived from an ancient enzyme; not in LUCA |
Aminoalkyl transfer 1 | Nicotianamine synthase, EC:2.5.1.43 | Rossmann-fold methyltransferase family with permuted order of sequence motifs | Derived from an ancient enzyme; not in LUCA |
 | ACC synthase, EC:4.4.1.14 | PLP-dependent aminotransferase fold; the SAM-binding domain is derived from generic substrate-binding cleft | Derived from an ancient enzyme; not in LUCA |
 | Acyl-homoserine lactone synthase, EC:6.1.- | GNAT-type acetyltransferase fold; the SAM-binding domain is derived from generic substrate-binding cleft | Derived from an ancient enzyme; not in LUCA |
Aminopropyl transfer | Spermidine synthase, EC:2.5.1.16 | Rossmann-fold methyltransferase family, but the substrate is decarboxy-SAM | Probably in LUCA |
Ribosyl transfer | tRNA-ribosyl transferase-isomerase, EC:5.- | QueA family; smaller β-barrel N-terminal domain and a larger C-terminal domain with α/β fold, distantly related to a TIM-barrel | Bacterial invention; not in LUCA |
5'deoxyadenosyl transfer | 5'-fluoro-5'-deoxy-adenosine synthase, EC:2.5.1.63 | Two-domains; larger N-terminal domain has distant similarity to Rossmann-fold methyltransferases, smaller C-terminal domain is a β-barrel | Bacterial invention; not in LUCA |
5'deoxyadenosyl radical synthesis | SAM radical enzymes | TIM-like α/β barrel with additional inserted elements. May have distant sequence similarity to TIM barrel of corrinoid methyltransferase (see text) | Probably in LUCA |
SAM decarboxylation | SAM decarboxylase, EC:4.1.1.50 | α/β/β/α sandwich in eukaryotes, apparently produced by duplication of a half-unit; stand-alone half-units exist in many bacteria and archaea | Probably in LUCA |
De novo SAM synthesis | Methionine adenosyl transferase, EC:2.5.1.6 | Unique fold: repeat of 3 β-α-β-β-α-β units | Probably in LUCA |
Regulatory binding of SAM | Methionine repressor | All-α SAM-binding domain is derived from generic small molecule-binding domain | Bacterial innovation |
 | CBS domain | Mostly-β SAM-binding domain is derived from generic small molecule-binding domain | Not in LUCA |
 | Transcription factor mtTFB | Rossmann-fold methyltransferase family member that has lost catalytic activity |  |