Escherichia coli K-12 substr. MG1655 Enzyme: selenocysteine synthase

Gene: selA Accession Numbers: EG10941 (EcoCyc), b3591, ECK3580

Synonyms: fdhA

Regulation Summary Diagram: ?

Regulation summary diagram for selA

Subunit composition of selenocysteine synthase = [SelA]10
         selenocysteine synthase = SelA

Selenocysteine synthase catalyzes the conversion of serine to selenocysteine on serine-charged tRNASec [Forchhammer91]. SelA is a complex of 10 subunits arranged in two rings [Engelhardt92]; the homodecameric structure is assembled via stepwise addition of dimers to intermediate oligomeric states [Manzine12].

The pyridoxal 5'-phosphate cofactor is present at a stoichiometry of one per monomer [Forchhammer91] and is attached at Lys295 [Tormay98]. The seryl-tRNASecUCA substrate is present at a stoichiometry of one per two monomers [Forchhammer91a]. The serine residue of seryl-tRNASec first forms a Schiff base with the PLP cofactor, followed by dehydration of serine to generate the enzyme-bound aminoacrylyl-tRNASec intermediate [Forchhammer91a].

A selA or selD mutant exhibits a defect in selenocysteinyl-tRNA formation, whereas a selB mutant does not [Leinfelder89].

Extracts of cells overproducing SelA and SelD exhibit in vitro production of selenocysteinyl-tRNAUCA from seryl-tRNAUCA [Leinfelder90].

Transcription of selAB appears to be constitutive [Sawers91]. A SECIS-like element in the 5' UTR of the selAB transcript binds a complex of SelB-GTP-selenocysteyl-tRNASec and negatively regulates efficiency of translation initiation, thus coupling the biosynthesis of selenocysteine to the availability of selenium [Thanbichler02]. SelA protein levels are decreased when E. coli is grown in media with high levels of zinc [Easton06].

SelA: "selenocysteine A" [Leinfelder88]

Review: [Jiang02]

Gene Citations: [Forchhammer91b]

Locations: cytosol

Map Position: [3,757,881 <- 3,759,272] (80.99 centisomes, 292°)
Length: 1392 bp / 463 aa

Molecular Weight of Polypeptide: 50.607 kD (from nucleotide sequence), 51.0 kD (experimental) [Forchhammer91 ]

Molecular Weight of Multimer: 500.0 kD (experimental) [Manzine12]

Unification Links: ASAP:ABE-0011731 , CGSC:785 , DIP:DIP-10847N , EchoBASE:EB0934 , EcoGene:EG10941 , EcoliWiki:b3591 , ModBase:P0A821 , OU-Microarray:b3591 , PortEco:selA , PR:PRO_000023931 , Pride:P0A821 , Protein Model Portal:P0A821 , RefSeq:NP_418048 , RegulonDB:EG10941 , SMR:P0A821 , String:511145.b3591 , UniProt:P0A821

Relationship Links: InterPro:IN-FAMILY:IPR004534 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR018319 , InterPro:IN-FAMILY:IPR025862 , Pfam:IN-FAMILY:PF03841 , Pfam:IN-FAMILY:PF12390

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for selA

GO Terms:

Biological Process: GO:0016260 - selenocysteine biosynthetic process Inferred from experiment [Leinfelder88]
GO:0097056 - selenocysteinyl-tRNA(Sec) biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Forchhammer91]
GO:0001514 - selenocysteine incorporation Inferred by computational analysis [GOA06, GOA01a]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004125 - L-seryl-tRNASec selenium transferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Forchhammer91]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01a, Forchhammer91]
GO:0042802 - identical protein binding Inferred from experiment [Forchhammer91]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]


Essentiality data for selA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Last-Curated ? 31-Dec-2012 by Keseler I , SRI International

Enzymatic reaction of: selenocysteine synthase

EC Number:

selenophosphate + an L-seryl-[tRNAsec] <=> an L-selenocysteinyl-[tRNAsec] + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: L-selenocysteine biosynthesis I (bacteria)

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Forchhammer91]

Inhibitors (Unknown Mechanism): borohydride [Forchhammer91b] , cyanide [Forchhammer91b]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
0.022, 0.022
0.072, 0.072
[Tormay98, BRENDA14]

Sequence Features

Protein sequence of selenocysteine synthase with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 7
[Forchhammer91, UniProt10b]
UniProt: (in Ref. 1; AAA24624);
Mutagenesis-Variant 224
[Tormay98, UniProt11]
UniProt: Still binds PLP.
N6-pyridoxal-phosphate-Lys-Modification 295
[Tormay98, UniProt15]
UniProt: N6-(pyridoxal phosphate)lysine.
Mutagenesis-Variant 295
[Tormay98, UniProt11]
UniProt: Loss of activity and PLP binding.
Mutagenesis-Variant 328
[Tormay98, UniProt11]
UniProt: Loss of PLP binding.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3591 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10941; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Easton06: Easton JA, Thompson P, Crowder MW (2006). "Time-dependent translational response of E. coli to excess Zn(II)." J Biomol Tech 17(5);303-7. PMID: 17122063

Engelhardt92: Engelhardt H, Forchhammer K, Muller S, Goldie KN, Bock A (1992). "Structure of selenocysteine synthase from Escherichia coli and location of tRNA in the seryl-tRNA(sec)-enzyme complex." Mol Microbiol 6(23);3461-7. PMID: 1474891

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Forchhammer91: Forchhammer K, Leinfelder W, Boesmiller K, Veprek B, Bock A (1991). "Selenocysteine synthase from Escherichia coli. Nucleotide sequence of the gene (selA) and purification of the protein." J Biol Chem 266(10);6318-23. PMID: 2007584

Forchhammer91a: Forchhammer K, Bock A (1991). "Selenocysteine synthase from Escherichia coli. Analysis of the reaction sequence." J Biol Chem 266(10);6324-8. PMID: 2007585

Forchhammer91b: Forchhammer K, Boesmiller K, Bock A (1991). "The function of selenocysteine synthase and SELB in the synthesis and incorporation of selenocysteine." Biochimie 1991;73(12);1481-6. PMID: 1839607

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Jiang02: Jiang ZH, Mu Y, Li WJ, Yan GL, Luo GM (2002). "The progress in mechanism of selenoprotein biosynthesis." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 34(4);395-9. PMID: 12098758

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Leinfelder88: Leinfelder W, Forchhammer K, Zinoni F, Sawers G, Mandrand-Berthelot MA, Bock A (1988). "Escherichia coli genes whose products are involved in selenium metabolism." J Bacteriol 170(2);540-6. PMID: 2962989

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

Leinfelder90: Leinfelder W, Forchhammer K, Veprek B, Zehelein E, Bock A (1990). "In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product." Proc Natl Acad Sci U S A 1990;87(2);543-7. PMID: 2405383

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Manzine12: Manzine LR, Cassago A, da Silva MT, Thiemann OH (2012). "An efficient protocol for the production of tRNA-free recombinant Selenocysteine Synthase (SELA) from Escherichia coli and its biophysical characterization." Protein Expr Purif 88(1);80-84. PMID: 23266652

Sawers91: Sawers G, Heider J, Zehelein E, Bock A (1991). "Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme." J Bacteriol 1991;173(16);4983-93. PMID: 1650339

Thanbichler02: Thanbichler M, Bock A (2002). "The function of SECIS RNA in translational control of gene expression in Escherichia coli." EMBO J 21(24);6925-34. PMID: 12486013

Tormay98: Tormay P, Wilting R, Lottspeich F, Mehta PK, Christen P, Bock A (1998). "Bacterial selenocysteine synthase--structural and functional properties." Eur J Biochem 254(3);655-61. PMID: 9688279

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon May 4, 2015, biocyc11.