Genome Property Definition Page

Nameselenocysteine system
DescriptionThe property of incorporating selenocysteine as an alternate amino acid during protein translation from mRNA. The site of incorporation often aligns to an active site Cys residue of a homologous protein in a selenocysteine-negative species. One required element is a selenocysteine-specific tRNA (selC) to recognize a TGA codon in the appropriate context. Two required proteins are a selenocysteine-specific elongation factor (SelB), and a selenium donor protein (selD) that may participate in other systems in addition or instead (selenouridine biosynthesis, and selenium-dependent molybdenum hydroxylase maturation). Finally, a mechanism for converting the serine placed on selenocysteine-specific tRNA into selenocysteine is required. This is achieved by seryl-t RNA(sec) selenium transferase (SelA) in bacteria, but in a two-step process starting with phosphorylation in the Archaea and Eukaryota. Note that SelD may itself be a selenoprotein, and so may appear truncated by a stop codon, thus not triggering the rule to assign the selenocysteine property automatically. Before the state of this property is set to "YES", an example of a potential selenocysteine-containing protein must be manually annotated. Commonly observed selenoproteins include the selenium donor protein SelD (selenide, water dikinase) and subunits of formate dehydrogenase, thioredoxin reductase, glycine reductase, heterodisulfide reductase, methylviologen-reducing hydrogenase and glutathione peroxidase. In certain species all components of the system can be found save the SelC tRNA (including examples) even after a manual search. These are given the state "PARTIAL" to indicate the possibility that either the ability to incorporate selenocysteine has been lost (and the examples are actually truncated or not expressed) or an as-of-yet undescribed tRNA system exists in these species. The selenium donor protein seems to occur in some species that lack the selenium-specific tRNA, elongation factor, and transferase. This usually reflects the incorporation of selenium into certain tRNAs. Note also that selenium is sometimes used to label proteins in vitro, so not every literature reference to selenocysteine implies incorporation during translation. An analogous system, discovered more recently, incorporates pyrrolysine at specific TAG codons.
Parent PropertyGenProp0075: protein modification, prosthetic groups and cofactors
GenProp0126: amino acid biosynthesis
GenProp0197: protein biosynthesis
Web ReferencesKEGG: Selenoamino Acid Metabolism
Gene Ontology TermGO:0001514: selenocysteine incorporation (biological_process)
GO:0001514: selenocysteine incorporation (biological_process)
GO:0016260: selenocysteine biosynthetic process (biological_process)
GO:0030533: triplet codon-amino acid adaptor activity (molecular_function)

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
selenocysteine-containing proteinsexampleYESSELENO_CYS (att_type)
Sec-tRNA(Sec) synthesisselAYESTIGR00474 (HMM): L-seryl-tRNA(Sec) selenium transferaseGenProp0797 (GENPROP): selenocysteinyl-tRNA, PSTK/SepSecS pathway
GO:0016260: selenocysteine biosynthetic process
GO:0001514: selenocysteine incorporation
GO:0016260: selenocysteine biosynthetic process
GO:0001514: selenocysteine incorporation
selenocysteine-specific translation elongation factorselBYESTIGR00475 (HMM): selenocysteine-specific translation elongation factorGO:0001514: selenocysteine incorporation
selenocysteine-specific tRNA (tRNA-SeC)selCYEStRNA-SeC (RNA)
GO:0030533: triplet codon-amino acid adaptor activity
selenide, water dikinaseselDYESTIGR00476 (HMM): selenide, water dikinaseGO:0016260: selenocysteine biosynthetic process
GO:0001514: selenocysteine incorporation

Parent Properties
GenProp0075protein modification, prosthetic groups and cofactors
GenProp0126amino acid biosynthesis
GenProp0197protein biosynthesis

Sibling Properties
GenProp0002coenzyme F420 utilization
GenProp0061lipoprotein system lgt/lsp/lnt
GenProp0127Tat (Sec-independent) protein export
GenProp0284cobalamin-utilizing enzymes
GenProp0295prokaryotic N-terminal cleavage/methylation, type IV pilin-like
GenProp0726selenium-dependent molybdenum hydroxylase system
GenProp0745lipoyl-protein attachment
GenProp0860tryptophan tryptophylquinone modification of methylamine dehydrogenase
GenProp0918anaerobic sulfatase/maturase system
GenProp0923mycothiol system
GenProp0933bacillithiol utilization
GenProp0938glycine radical enzyme system, YjjI/YjjW pair
GenProp0943pyruvate formate-lyase system
GenProp0001chorismate biosynthesis via shikimate
GenProp0037tryptophan biosynthesis from ribose-5-phosphate
GenProp0039phenylalanine biosynthesis from chorismate
GenProp0045tyrosine biosynthesis from chorismate
GenProp0087arginine biosynthesis from glutatmate via N-acetylglutamate
GenProp0109histidine biosynthesis from ribose-5-phosphate
GenProp0111proline biosynthesis from glutamate
GenProp0117arginine biosynthesis from ornithine, carbamoyl-p and aspartate
GenProp0118ornithine biosynthesis from glutamate, acetylated branch
GenProp0159threonine biosynthesis from aspartate semialdehyde
GenProp0160aspartate semialdehyde biosynthesis from aspartate
GenProp0161methionine biosynthesis from homoserine
GenProp0162isoleucine biosynthesis from threonine and pyruvate
GenProp0163valine biosynthesis from pyruvate
GenProp0164leucine biosynthesis from pyruvate and acetyl-CoA
GenProp0178glycine cleavage system
GenProp0199lysine biosynthesis
GenProp0304cysteine biosynthesis, tRNA-dependent
GenProp0305cysteine biosynthesis
GenProp0729methionine salvage from methylthioadenosine
GenProp0797selenocysteinyl-tRNA, PSTK/SepSecS pathway
GenProp0132transcription termination - antitermination Nus factors
GenProp0148release factor 2 programmed frameshift
GenProp0174ribosome, bacterial, large subunit
GenProp0175ribosome, bacterial, small subunit
GenProp0188GatABC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase complex
GenProp0189tRNA-Gln direct aminoacylation
GenProp0211tmRNA trans-translation system
GenProp0258tRNA aminoacylation
GenProp0259tRNA-Asn direct aminoacylation
GenProp0634Sigma-54 (RpoN) systems
GenProp0692selenouridine-containing tRNA
GenProp0704tRNA U34 carboxymethylaminomethyl modification
GenProp0740translation initiation, bacterial
GenProp0741translation elongation, bacterial
GenProp0746translation termination, bacterial
GenProp0812rho-dependent termination