Pathways & interactions
(Uracil-5)-methyltransferase family (IPR010280)
Short name: U5_MeTrfase_fam
Overlapping homologous superfamilies
- (Uracil-5)-methyltransferase family (IPR010280)
- 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (IPR001566)
- 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC (IPR011825)
- tRNA (uracil-5-)-methyltransferase (IPR025795)
- tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA (IPR011869)
This family consists of (uracil-5-)-methyltransferases EC:220.127.116.11 from bacteria, archaea and eukaryotes. They are class I-like SAM-binding methyltransferases.
Methyltransferases (MTs) (EC 2.1.1.-) constitute an important class of enzymes present in every life form. They transfer a methyl group most frequently from S-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such as nitrogen, oxygen, sulfur or carbon leading to S-adenosyl-L-homocysteine (AdoHcy) and a methylated molecule. The substrates that are methylated by these enzymes cover virtually every kind of biomolecules ranging from small molecules, to lipids, proteins and nucleic acids. MTs are therefore involved in many essential cellular processes including biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing [PMID: 16225687, PMID: 12826405, PMID: 21858014].
More than 230 different enzymatic reactions of MTs have been described so far, of which more than 220 use SAM as the methyl donor. A review published in 2003 [PMID: 12826405] divides all MTs into 5 classes based on the structure of their catalytic domain (fold):
- class I: Rossmann-like alpha/beta
- class II: TIM beta/alpha-barrel alpha/beta
- class III: tetrapyrrole methylase alpha/beta
- class IV: SPOUT alpha/beta
- class V: SET domain all beta
A more recent paper [PMID: 21858014] based on a study of the Saccharomyces cerevisiae methyltransferome argues for four more folds:
- class VI: transmembrane all alpha
- class VII: DNA/RNA-binding 3-helical bundle all alpha
- class VIII: SSo0622-like alpha+beta
- class IX: thymidylate synthetase alpha+beta
The vast majority of MTs belong to the Rossmann-like fold (Class I) which consists in a seven-stranded beta sheet adjoined by alpha helices. The beta sheet contains a central topological switch-point resulting in a deep cleft in which SAM binds. Class I MTs display two conserved positions, the first one is a GxGxG motif (or at least a GxG motif) at the end of the first beta strand which is characteristic of a nucleotide-binding site and is hence used to bind the adenosyl part of SAM, the second conserved position is an acidic residue at the end of the second beta strand that forms one hydrogen bond to each hydroxyl of the SAM ribose part. The core of these enzymes is composed by about 150 amino acids that show very strong spatial conservation. Catechol O- MT (EC 18.104.22.168) is the canonical Class I MT considering that it consists in the exact consensus structural core with no extra domain [PMID: 12826405].