Subsystem Info

Name:RidA family in 981 representative prokaryotes
Author:Niehaus_Tom_user
Version:182
Last Modified:11-2-2014:23:4:52
Literature
Websites
DescriptionThis Subsystem has been encoded for the publication "Genomic and experimental evidence for multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family" (Niehaus et al., 2014)

You are now in the Subsystem viewer of the SEED database. The narrow green banner above provides links to genome analysis tools and data. Please use them to see -

I. The “Spreadsheet” Tab: contains a Table where each row represents a genome, each column corresponds to a Functional Role (protein family), and each cell is populated with the gene(s)/protein(s) that implement this Functional Role in each organism. Each gene/protein is identified with a blue number – the Protein-Encoding Gene (PEG) ID - which is linked to an underlying detailed PEG page. The Spreadsheet can be sorted (by taxonomy, by organism, by the pattern of PEGs absence/presence, or by gene clustering pattern) or filtered (use column headings). Cells highlighted with the same color within the same row (genome) indicate genes that are co-localized on the chromosome.

II. The “Functional Roles” Tab: contains the list of protein families included in this Subsystem, and explains abbreviations used in the heading of the Subsystem Spreadsheet. Note "Subsets" (in the leftmost column), which group some Functional Roles together. Subsets allow to limit Subsystem Spreadsheet view to those columns that are included in a selected SubSet . Use "Limit Display" tab on the “Spreadsheet” page to do this

III. Further help in navigating the SEED database is available here -
SEED_Viewer_Tutorial
Glossary

NotesThis Subsystem has been encoded for the publication "Genomic and experimental evidence for multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family" (Niehaus et al., 2014)

Background
It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5'-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.
Results
Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5'-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.
Conclusions
Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5'-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.
Variants
VariantDescription
Classification:Metabolite damage and its repair or mitigation