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Table 1 Classes of SAM binding proteins

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  
  1. 1 An additional reaction in this class is synthesis of acp3U, a modified base in some tRNAs and rRNAs. This amino alkyl transfer requires SAM, but responsible protein has not been identified.