Genome Property Definition Page
| Accession | GenProp0016 |
| Name | selenocysteine system |
| Type | SYSTEM |
| Description | The 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 Property | GenProp0075: protein modification, prosthetic groups and cofactors GenProp0126: amino acid biosynthesis GenProp0197: protein biosynthesis |
| Web References | KEGG: Selenoamino Acid Metabolism |
| Gene Ontology Term | GO: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) |
Components
| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|---|---|---|---|
| selenocysteine-containing proteins | example | YES | SELENO_CYS (att_type) | |
| Sec-tRNA(Sec) synthesis | selA | YES | TIGR00474 (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 factor | selB | YES | TIGR00475 (HMM): selenocysteine-specific translation elongation factor | GO:0001514: selenocysteine incorporation |
| selenocysteine-specific tRNA (tRNA-SeC) | selC | YES | tRNA-SeC (RNA) | GO:0030533: triplet codon-amino acid adaptor activity |
| selenide, water dikinase | selD | YES | TIGR00476 (HMM): selenide, water dikinase | GO:0016260: selenocysteine biosynthetic process GO:0001514: selenocysteine incorporation |
Parent Properties
| Accession | Name |
|---|---|
| GenProp0075 | protein modification, prosthetic groups and cofactors |
| GenProp0126 | amino acid biosynthesis |
| GenProp0197 | protein biosynthesis |
Sibling Properties
| Accession | Name |
|---|---|
| GenProp0002 | coenzyme F420 utilization |
| GenProp0061 | lipoprotein system lgt/lsp/lnt |
| GenProp0127 | Tat (Sec-independent) protein export |
| GenProp0284 | cobalamin-utilizing enzymes |
| GenProp0295 | prokaryotic N-terminal cleavage/methylation, type IV pilin-like |
| GenProp0726 | selenium-dependent molybdenum hydroxylase system |
| GenProp0745 | lipoyl-protein attachment |
| GenProp0860 | tryptophan tryptophylquinone modification of methylamine dehydrogenase |
| GenProp0918 | anaerobic sulfatase/maturase system |
| GenProp0923 | mycothiol system |
| GenProp0933 | bacillithiol utilization |
| GenProp0938 | glycine radical enzyme system, YjjI/YjjW pair |
| GenProp0943 | pyruvate formate-lyase system |
| GenProp0001 | chorismate biosynthesis via shikimate |
| GenProp0037 | tryptophan biosynthesis from ribose-5-phosphate |
| GenProp0039 | phenylalanine biosynthesis from chorismate |
| GenProp0045 | tyrosine biosynthesis from chorismate |
| GenProp0087 | arginine biosynthesis from glutatmate via N-acetylglutamate |
| GenProp0109 | histidine biosynthesis from ribose-5-phosphate |
| GenProp0111 | proline biosynthesis from glutamate |
| GenProp0117 | arginine biosynthesis from ornithine, carbamoyl-p and aspartate |
| GenProp0118 | ornithine biosynthesis from glutamate, acetylated branch |
| GenProp0159 | threonine biosynthesis from aspartate semialdehyde |
| GenProp0160 | aspartate semialdehyde biosynthesis from aspartate |
| GenProp0161 | methionine biosynthesis from homoserine |
| GenProp0162 | isoleucine biosynthesis from threonine and pyruvate |
| GenProp0163 | valine biosynthesis from pyruvate |
| GenProp0164 | leucine biosynthesis from pyruvate and acetyl-CoA |
| GenProp0178 | glycine cleavage system |
| GenProp0199 | lysine biosynthesis |
| GenProp0304 | cysteine biosynthesis, tRNA-dependent |
| GenProp0305 | cysteine biosynthesis |
| GenProp0729 | methionine salvage from methylthioadenosine |
| GenProp0797 | selenocysteinyl-tRNA, PSTK/SepSecS pathway |
| GenProp0312 | pyrrolysine |
| GenProp0132 | transcription termination - antitermination Nus factors |
| GenProp0148 | release factor 2 programmed frameshift |
| GenProp0174 | ribosome, bacterial, large subunit |
| GenProp0175 | ribosome, bacterial, small subunit |
| GenProp0188 | GatABC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase complex |
| GenProp0189 | tRNA-Gln direct aminoacylation |
| GenProp0211 | tmRNA trans-translation system |
| GenProp0258 | tRNA aminoacylation |
| GenProp0259 | tRNA-Asn direct aminoacylation |
| GenProp0634 | Sigma-54 (RpoN) systems |
| GenProp0692 | selenouridine-containing tRNA |
| GenProp0704 | tRNA U34 carboxymethylaminomethyl modification |
| GenProp0740 | translation initiation, bacterial |
| GenProp0741 | translation elongation, bacterial |
| GenProp0746 | translation termination, bacterial |
| GenProp0812 | rho-dependent termination |