GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.

Have any questions? Please email us at ecoliwiki@gmail.com

PMID:21858014

From GONUTS
Jump to: navigation, search
Citation

Wlodarski, T, Kutner, J, Towpik, J, Knizewski, L, Rychlewski, L, Kudlicki, A, Rowicka, M, Dziembowski, A and Ginalski, K (2011) Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PLoS ONE 6:e23168

Abstract

Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity). Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

Links

PubMed PMC3153492 Online version:10.1371/journal.pone.0023168

Keywords

Catalytic Domain; Electrophoresis, Polyacrylamide Gel; Genome, Fungal; Methylation; Methyltransferases/chemistry; Methyltransferases/genetics; Methyltransferases/metabolism; Multigene Family; Mutation; Proteome/genetics; Proteome/metabolism; RNA, Fungal/metabolism; Saccharomyces cerevisiae/enzymology; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae Proteins/classification; Saccharomyces cerevisiae Proteins/genetics; Saccharomyces cerevisiae Proteins/metabolism; Structure-Activity Relationship; Substrate Specificity

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

YEAST:EFM2

enables

GO:0008757: S-adenosylmethionine-dependent methyltransferase activity

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

YEAST:BMT5

enables

GO:0008757: S-adenosylmethionine-dependent methyltransferase activity

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

YEAST:YG5X

involved_in

GO:0032259: methylation

ECO:0000305: curator inference used in manual assertion

GO:0008168

P

Seeded From UniProt

complete

YEAST:YG5X

enables

GO:0008168: methyltransferase activity

ECO:0000250: sequence similarity evidence used in manual assertion

UniProtKB:Q12314

F

Seeded From UniProt

complete

YEAST:YM91

involved_in

GO:0032259: methylation

ECO:0000305: curator inference used in manual assertion

GO:0008168

P

Seeded From UniProt

complete

YEAST:YM91

enables

GO:0008168: methyltransferase activity

ECO:0000250: sequence similarity evidence used in manual assertion

UniProtKB:Q12314

F

Seeded From UniProt

complete

YEAST:EFM7

enables

GO:0008757: S-adenosylmethionine-dependent methyltransferase activity

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete


See also

References

See Help:References for how to manage references in GONUTS.