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MetaCyc Pathway: L-selenocysteine biosynthesis II (archaea and eukaryotes)
Inferred from experimentTraceable author statement to experimental support

Enzyme View:

Pathway diagram: L-selenocysteine biosynthesis II (archaea and eukaryotes)

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisAmino Acids BiosynthesisProteinogenic Amino Acids BiosynthesisL-selenocysteine Biosynthesis

Some taxa known to possess this pathway include : Bos taurus, Gallus gallus, Homo sapiens, Methanocaldococcus jannaschii, Methanococcus maripaludis, Methanococcus vannielii, Mus musculus

Expected Taxonomic Range: Archaea, Eukaryota

General Background

Se0 is an essential trace element for many (but not all) organisms from all domains of life. For example among animals, mammals require selenium but some protists, such as Trypanosoma brucei, do not [Aeby09]. The green alga Chlamydomonas reinhardii contains selenoproteins, but land plants and yeast do not [Novoselov02]. The best studied biological form of Se0 is the amino acid L-selenocysteine (sec). The compound display pages for Se0 and L-selenocysteine show links to enzymes in MetaCyc for which Se0 is functionally important. In addition, see EC, EC, EC and EC Se0 is also present in selenonucleosides that have been identified in bacterial tRNAs. Reviewed in [Stock09].

In L-selenocysteine the thiol group of L-cysteine is replaced by a selenol group. L-selenocysteine is considered to be the 21st genetically encoded amino acid because it is co-translationally inserted into nacent polypeptide chains at an in-frame UGA nonsnense codon in the mRNA. This is done by a decoding mechanism that involves a selenocysteine insertion sequence (SECIS) element in the mRNA and coordinated interactions between RNA-protein complexes. A model for the role of these cytoplasmic and nuclear supramolecular complex interactions in L-selenocysteine biosynthesis has been proposed [SmallHoward06]. The function of L-selenocysteine in proteins remains to be completely defined, although its occurrence in the active site of some redox-active enzymes suggests a role in their catalytic mechanism. There are two known pathways for selenocysteine biosynthesis. One is found in bacteria (see pathway L-selenocysteine biosynthesis I (bacteria)) and the other is found in archaea and eukaryotes (this pathway), which has interesting phylogenetic implications. Reviewed in [Stock09].

About This Pathway

The pathway shown here is found in some archaea and eukaryotes, the best studied organisms being certain methanogens, and mammals [Xu07a]. It is an indirect, tRNA-dependent pathway for amino acid biosynthesis in which the amino acid is synthesized on its tRNA. A non-cognate amino acid is first attached to the tRNA and is then converted to the cognate amino acid by tRNA-dependent modifying enzymes. Other examples of an indirect, tRNA-dependent amino acid biosynthetic pathway are L-asparagine biosynthesis III (tRNA-dependent) and glutaminyl-tRNAgln biosynthesis via transamidation (as compared with tRNA charging).

The difference between this pathway and the bacterial L-selenocysteine biosynthetic pathway ( L-selenocysteine biosynthesis I (bacteria)) is that in bacteria an L-seryl-[tRNAsec] is directly converted to an L-selenocysteinyl-[tRNAsec], whereas in archaea and eukaryotes an L-seryl-[tRNAsec] is first converted to an O-phospho-L-seryl-[tRNASec] by a kinase and the O-phosphoserine-containing product is transformed to L-selenocysteine by SepSecS. In both pathways, selenophosphate is the Se0 donor, synthesized from hydrogen selenide and ATP by selenophosphate synthetase (in [Xu07b]). Reviewed in [Stock09, Sheppard08, Xu07].

In this pathway of L-selenocysteine biosynthesis on a tRNAsec, a tRNAsec is charged with L-serine. The seryl moiety of the an L-seryl-[tRNAsec] formed is phosphorylated by O-phosphoseryl-tRNAsec kinase to form an an O-phospho-L-seryl-[tRNASec] intermediate which is then modified to an L-selenocysteinyl-[tRNAsec] by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase. Thus, the backbone for L-selenocysteine is L-serine. Although the pathway is identical in archaea and eukaryota, a difference between them in a tRNAsec identity elements for the phosphorylation reaction has been found. Reviewed in [Sheppard08, Xu07].

The seryl-tRNA synthetase step in this pathway is shared among bacteria, archaea and eukaryota. However, this pathway then diverges from the bacterial pathway. In the bacterial L-selenocysteine biosynthetic pathway selenocysteine synthase converts an L-seryl-[tRNAsec] to an L-selenocysteinyl-[tRNAsec] and L-selenocysteine is incorporated into proteins using an RNA element that facilitates UGA recognition and the selenocysteine-specific elongation factor SelB (see pathway L-selenocysteine biosynthesis I (bacteria)). In this archaeal and eukaryotic pathway an L-seryl-[tRNAsec] is first converted to an O-phospho-L-seryl-[tRNASec] by O-phosphoseryl-tRNAsec kinase and the bound 3-phospho-L-serine is converted to L-selenocysteine by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase using selenophosphate. Reviewed in [Sheppard08, Xu07].

Variants: L-selenocysteine biosynthesis I (bacteria)

Relationship Links: KEGG:PART-OF:map00970

Created 24-Jun-2009 by Fulcher CA, SRI International


Aeby09: Aeby E, Palioura S, Pusnik M, Marazzi J, Lieberman A, Ullu E, Soll D, Schneider A (2009). "The canonical pathway for selenocysteine insertion is dispensable in Trypanosomes." Proc Natl Acad Sci U S A 106(13);5088-92. PMID: 19279205

Baron90: Baron C, Heider J, Bock A (1990). "Mutagenesis of selC, the gene for the selenocysteine-inserting tRNA-species in E. coli: effects on in vivo function." Nucleic Acids Res 18(23);6761-6. PMID: 1702199

Baron91: Baron C, Bock A (1991). "The length of the aminoacyl-acceptor stem of the selenocysteine-specific tRNA(Sec) of Escherichia coli is the determinant for binding to elongation factors SELB or Tu." J Biol Chem 266(30);20375-9. PMID: 1939093

Baron93: Baron C, Westhof E, Bock A, Giege R (1993). "Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser)." J Mol Biol 231(2);274-92. PMID: 8510147

Berg91: Berg BL, Baron C, Stewart V (1991). "Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. II. Evidence that a mRNA stem-loop structure is essential for decoding opal (UGA) as selenocysteine." J Biol Chem 266(33);22386-91. PMID: 1834670

Forchhammer89: Forchhammer K, Leinfelder W, Bock A (1989). "Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein." Nature 342(6248);453-6. PMID: 2531290

Forchhammer91: Forchhammer K, Boesmiller K, Bock A (1991). "The function of selenocysteine synthase and SELB in the synthesis and incorporation of selenocysteine." Biochimie 73(12);1481-6. PMID: 1839607

Forster90: Forster C, Ott G, Forchhammer K, Sprinzl M (1990). "Interaction of a selenocysteine-incorporating tRNA with elongation factor Tu from E.coli." Nucleic Acids Res 18(3);487-91. PMID: 2408012

Heider92: Heider J, Baron C, Bock A (1992). "Coding from a distance: dissection of the mRNA determinants required for the incorporation of selenocysteine into protein." EMBO J 11(10);3759-66. PMID: 1396569

Leinfelder88: Leinfelder W, Zehelein E, Mandrand-Berthelot MA, Bock A (1988). "Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine." Nature 331(6158);723-5. PMID: 2963963

Leinfelder89: Leinfelder W, Stadtman TC, Bock A (1989). "Occurrence in vivo of selenocysteyl-tRNA(SERUCA) in Escherichia coli. Effect of sel mutations." J Biol Chem 264(17);9720-3. PMID: 2524495

Li92c: Li WQ, Yarus M (1992). "Bar to normal UGA translation by the selenocysteine tRNA." J Mol Biol 223(1);9-15. PMID: 1370545

Novoselov02: Novoselov SV, Rao M, Onoshko NV, Zhi H, Kryukov GV, Xiang Y, Weeks DP, Hatfield DL, Gladyshev VN (2002). "Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii." EMBO J 21(14);3681-93. PMID: 12110581

Schon89: Schon A, Bock A, Ott G, Sprinzl M, Soll D (1989). "The selenocysteine-inserting opal suppressor serine tRNA from E. coli is highly unusual in structure and modification." Nucleic Acids Res 17(18);7159-65. PMID: 2529478

Sheppard08: Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Soll D (2008). "From one amino acid to another: tRNA-dependent amino acid biosynthesis." Nucleic Acids Res 36(6);1813-25. PMID: 18252769

Siekevitz81: Siekevitz P, Zamecnik PC (1981). "Ribosomes and protein synthesis." J Cell Biol 91(3 Pt 2);53s-65s. PMID: 7033244

SmallHoward06: Small-Howard A, Morozova N, Stoytcheva Z, Forry EP, Mansell JB, Harney JW, Carlson BA, Xu XM, Hatfield DL, Berry MJ (2006). "Supramolecular complexes mediate selenocysteine incorporation in vivo." Mol Cell Biol 26(6);2337-46. PMID: 16508009

Stock09: Stock T, Rother M (2009). "Selenoproteins in Archaea and Gram-positive bacteria." Biochim Biophys Acta. PMID: 19344749

Xu07: Xu XM, Carlson BA, Zhang Y, Mix H, Kryukov GV, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL (2007). "New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea." Biol Trace Elem Res 119(3);234-41. PMID: 17916946

Xu07a: Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL (2007). "Biosynthesis of selenocysteine on its tRNA in eukaryotes." PLoS Biol 5(1);e4. PMID: 17194211

Xu07b: Xu XM, Carlson BA, Irons R, Mix H, Zhong N, Gladyshev VN, Hatfield DL (2007). "Selenophosphate synthetase 2 is essential for selenoprotein biosynthesis." Biochem J 404(1);115-20. PMID: 17346238

Zinoni87: Zinoni F, Birkmann A, Leinfelder W, Bock A (1987). "Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon." Proc Natl Acad Sci U S A 84(10);3156-60. PMID: 3033637

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Araiso08: Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, Nureki O (2008). "Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation." Nucleic Acids Res 36(4);1187-99. PMID: 18158303

Bilokapic04: Bilokapic S, Korencic D, Soll D, Weygand-Durasevic I (2004). "The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species from all three kingdoms of life." Eur J Biochem 271(4);694-702. PMID: 14764085

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Carlson04: Carlson BA, Xu XM, Kryukov GV, Rao M, Berry MJ, Gladyshev VN, Hatfield DL (2004). "Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase." Proc Natl Acad Sci U S A 101(35);12848-53. PMID: 15317934

Costa00: Costa M, Rodriguez-Sanchez JL, Czaja AJ, Gelpi C (2000). "Isolation and characterization of cDNA encoding the antigenic protein of the human tRNP(Ser)Sec complex recognized by autoantibodies from patients withtype-1 autoimmune hepatitis." Clin Exp Immunol 121(2);364-74. PMID: 10931155

Ehrenreich92: Ehrenreich A, Forchhammer K, Tormay P, Veprek B, Bock A (1992). "Selenoprotein synthesis in E. coli. Purification and characterisation of the enzyme catalysing selenium activation." Eur J Biochem 206(3);767-73. PMID: 1606960

Ganichkin08: Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC (2008). "Structure and catalytic mechanism of eukaryotic selenocysteine synthase." J Biol Chem 283(9);5849-65. PMID: 18093968

Guimaraes96: Guimaraes MJ, Peterson D, Vicari A, Cocks BG, Copeland NG, Gilbert DJ, Jenkins NA, Ferrick DA, Kastelein RA, Bazan JF, Zlotnik A (1996). "Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism?." Proc Natl Acad Sci U S A 93(26);15086-91. PMID: 8986768

Herkel02: Herkel J, Heidrich B, Nieraad N, Wies I, Rother M, Lohse AW (2002). "Fine specificity of autoantibodies to soluble liver antigen and liver/pancreas." Hepatology 35(2);403-8. PMID: 11826415

Kaiser05: Kaiser JT, Gromadski K, Rother M, Engelhardt H, Rodnina MV, Wahl MC (2005). "Structural and functional investigation of a putative archaeal selenocysteine synthase." Biochemistry 44(40);13315-27. PMID: 16201757

Kim92: Kim IY, Veres Z, Stadtman TC (1992). "Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential for selenophosphate formation from ATP and selenide." J Biol Chem 267(27);19650-4. PMID: 1527085

Kim93: Kim IY, Veres Z, Stadtman TC (1993). "Biochemical analysis of Escherichia coli selenophosphate synthetase mutants. Lysine 20 is essential for catalytic activity and cysteine 17/19 for 8-azido-ATP derivatization." J Biol Chem 1993;268(36);27020-5. PMID: 8262938

Kim94: Kim IY, Stadtman TC (1994). "Effects of monovalent cations and divalent metal ions on Escherichia coli selenophosphate synthetase." Proc Natl Acad Sci U S A 91(15);7326-9. PMID: 8041789

Kim95a: Kim IY, Stadtman TC (1995). "Selenophosphate synthetase: detection in extracts of rat tissues by immunoblot assay and partial purification of the enzyme from the archaean Methanococcus vannielii." Proc Natl Acad Sci U S A 92(17);7710-3. PMID: 7644481

Lacourciere99: Lacourciere GM, Stadtman TC (1999). "Catalytic properties of selenophosphate synthetases: comparison of the selenocysteine-containing enzyme from Haemophilus influenzae with the corresponding cysteine-containing enzyme from Escherichia coli." Proc Natl Acad Sci U S A 96(1);44-8. PMID: 9874769

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Liu97a: Liu SY, Stadtman TC (1997). "Selenophosphate synthetase: enzyme labeling studies with [gamma-32P]ATP, [beta-32P]ATP, [8-14C]ATP, and [75Se]selenide." Arch Biochem Biophys 341(2);353-9. PMID: 9169026

Preabrazhenskay09: Preabrazhenskaya YV, Kim IY, Stadtman TC (2009). "Binding of ATP and its derivatives to selenophosphate synthetase from Escherichia coli." Biochemistry (Mosc) 74(8);910-6. PMID: 19817692

Sherrer08: Sherrer RL, O'Donoghue P, Soll D (2008). "Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation." Nucleic Acids Res 36(4);1247-59. PMID: 18174226

Suzuki08: Suzuki M, Lee DY, Inyamah N, Stadtman TC, Tjandra N (2008). "Solution NMR structure of selenium-binding protein from Methanococcus vannielii." J Biol Chem 283(38);25936-43. PMID: 18650445

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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