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MetaCyc Enzyme: selenocysteyl-tRNA-specific translation elongation factor

Gene: selB Accession Numbers: EG10942 (MetaCyc), b3590, ECK3579

Synonyms: fdhA

Species: Escherichia coli K-12 substr. MG1655

Component of: SelB-L-selenocysteinyl-tRNAsec

Summary:
SelB is a specialized translation factor that takes the place of elongation factor EF-Tu for the insertion of selenocysteine into a peptide chain at the site of a UGA codon. Most UGA codons signal chain termination; a UGA codon that encodes selenocysteine insertion is distinguished from those that signal chain termination by a structured sequence, called SECIS (SElenoCysteine Insertion Sequence), immediately downstream of the UGA codon [Heider92, Chen93d]. SelB recognizes and binds to identical bases within the loop region in the SECIS hairpin structure of both fdhF and fdnG mRNAs, and thereby brings the charged selenocysteyl-tRNASec (Sec-tRNASec) into the neighborhood of the UGA codon [Baron93, Ringquist94, Huttenhofer96].

SelB is found at a level of approximately 1100 copies per cell [Forchhammer90].

The N-terminal domain of SelB shares extensive sequence similarity with EF-Tu and IF2 [Forchhammer89]; this domain binds specifically to Sec-tRNASec [Kromayer96]. Its structure was modeled based on that of Thermus thermophilus EF-Tu [Hilgenfeld96]. Like EF-Tu, SelB binds GTP and exhibits a low GTPase activity which is stimulated by the presence of 70S ribosomes and the SECIS element [Huttenhofer98]. An additional C-terminal domain of SelB consisting of four tandem winged-helix motifs is responsible for binding to the SECIS mRNA structure [Kromayer96]. Suppressor mutations within selB that suppress the effect of defined mutations within the SECIS element have been isolated [Kromayer99, Li00b].

The kinetics of the interactions of SelB with guanosine nucleotides, the SECIS element, and Sec-tRNASec have been studied, shedding light on the mechanism of SelB action compared to the standard elongation factor EF-Tu [Thanbichler00, Paleskava10].

The length of the aminoacyl-acceptor stem of tRNASec is a specificity determinant for SelB binding [Baron91], and the selenol group of the aminoacylated tRNASec is required for stable interaction between SelB and Sec-tRNASec [Forchhammer91]. A crystal structure of a fragment of SelB in complex with the hairpin SECIS element has been solved at 2.3 Å resolution [Soler07].

A selB mutant accumulates Sec-tRNASecUCA and does not incorporate selenocysteine into selenoproteins [Leinfelder89].

SelB is able to autoregulate the expression of the selAB operon at the posttranscriptional level. SelB binds to a SECIS-like element upstream of the selA ribosome binding site, affecting the stability and translation of the selAB mRNA [Thanbichler02].

SelB: "selenium metabolism" [Leinfelder88a]

Reviews: [Stadtman91, Bock91, Bock97, Fagegaltier01, Thanbichler01]

Locations: cytosol

Map Position: [3,756,040 <- 3,757,884]

Molecular Weight of Polypeptide: 68.867 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011729 , CGSC:17890 , DIP:DIP-10848N , EchoBASE:EB0935 , EcoGene:EG10942 , EcoliWiki:b3590 , Mint:MINT-1221874 , ModBase:P14081 , OU-Microarray:b3590 , PortEco:selB , Pride:P14081 , Protein Model Portal:P14081 , RefSeq:NP_418047 , RegulonDB:EG10942 , SMR:P14081 , String:511145.b3590 , UniProt:P14081

Relationship Links: InterPro:IN-FAMILY:IPR000795 , InterPro:IN-FAMILY:IPR004161 , InterPro:IN-FAMILY:IPR004535 , InterPro:IN-FAMILY:IPR009000 , InterPro:IN-FAMILY:IPR009001 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR015190 , InterPro:IN-FAMILY:IPR015191 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2PJP , Pfam:IN-FAMILY:PF00009 , Pfam:IN-FAMILY:PF03144 , Pfam:IN-FAMILY:PF09106 , Pfam:IN-FAMILY:PF09107 , Prints:IN-FAMILY:PR00315 , Prosite:IN-FAMILY:PS00301 , Prosite:IN-FAMILY:PS51722

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0001514 - selenocysteine incorporation Inferred from experiment Inferred by computational analysis [GOA01, Leinfelder89]
GO:0016259 - selenocysteine metabolic process Inferred from experiment [Leinfelder88a]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment [Baron91]
GO:0003924 - GTPase activity Inferred from experiment Inferred by computational analysis [GOA01, Huttenhofer98]
GO:0005525 - GTP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Forchhammer89]
GO:0019003 - GDP binding Inferred from experiment [Forchhammer89]
GO:0035368 - selenocysteine insertion sequence binding Inferred from experiment [Baron93]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003746 - translation elongation factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA01]
GO:0005829 - cytosol

MultiFun Terms: information transfer protein related translation

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Enzymatic reaction of: GTPase (selenocysteyl-tRNA-specific translation elongation factor)

EC Number: 3.6.5.1/3.6.5.2/3.6.5.3/3.6.5.4/3.6.5.5/3.6.5.6

GTP + H2O <=> GDP + phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Summary:
The GTPase activity of SelB is stimulated by the presence of the 70S ribosome and the SECIS element [Huttenhofer98].

Kinetic Parameters:

Substrate
Km (μM)
Citations
GDP
13.4
[Thanbichler00]
GTP
0.74
[Thanbichler00]


Subunit of: SelB-L-selenocysteinyl-tRNAsec

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of SelB-L-selenocysteinyl-tRNAsec = [SelB][L-selenocysteinyl-tRNAsec]
         selenocysteyl-tRNA-specific translation elongation factor = SelB (extended summary available)

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 173
[UniProt14]
UniProt: tr-type G.
Nucleotide-Phosphate-Binding-Region 7 -> 14
[UniProt10]
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Protein-Segment 35 -> 39
[UniProt14]
UniProt: G2; Sequence Annotation Type: region of interest.
Protein-Segment 57 -> 60
[UniProt14]
UniProt: G3; Sequence Annotation Type: region of interest.
Nucleotide-Phosphate-Binding-Region 57 -> 61
[UniProt10]
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 112 -> 115
[UniProt10]
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Protein-Segment 147 -> 149
[UniProt14]
UniProt: G5; Sequence Annotation Type: region of interest.

History:
10/20/97 Gene b3590 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10942.


References

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, Heider J, Bock A (1993). "Interaction of translation factor SELB with the formate dehydrogenase H selenopolypeptide mRNA." Proc Natl Acad Sci U S A 90(9);4181-5. PMID: 8483932

Bock91: Bock A, Forchhammer K, Heider J, Baron C (1991). "Selenoprotein synthesis: an expansion of the genetic code." Trends Biochem Sci 16(12);463-7. PMID: 1838215

Bock97: Bock A, Hilgenfeld R, Tormay P, Wilting R, Kromayer M (1997). "Domain structure of the selenocysteine-specific translation factor SelB in prokaryotes." Biomed Environ Sci 10(2-3);125-8. PMID: 9315303

Chen93d: Chen GF, Fang L, Inouye M (1993). "Effect of the relative position of the UGA codon to the unique secondary structure in the fdhF mRNA on its decoding by selenocysteinyl tRNA in Escherichia coli." J Biol Chem 268(31);23128-31. PMID: 8226830

Fagegaltier01: Fagegaltier D, Carbon P, Krol A (2001). "Distinctive features in the SelB family of elongation factors for selenoprotein synthesis. A glimpse of an evolutionary complexified translation apparatus." Biofactors 14(1-4);5-10. PMID: 11568434

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

Forchhammer90: Forchhammer K, Rucknagel KP, Bock A (1990). "Purification and biochemical characterization of SELB, a translation factor involved in selenoprotein synthesis." J Biol Chem 265(16);9346-50. PMID: 2140572

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Hilgenfeld96: Hilgenfeld R, Bock A, Wilting R (1996). "Structural model for the selenocysteine-specific elongation factor SelB." Biochimie 78(11-12);971-8. PMID: 9150874

Huttenhofer96: Huttenhofer A, Westhof E, Bock A (1996). "Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SELB." RNA 2(4);354-66. PMID: 8634916

Huttenhofer98: Huttenhofer A, Bock A (1998). "Selenocysteine inserting RNA elements modulate GTP hydrolysis of elongation factor SelB." Biochemistry 37(3);885-90. PMID: 9454578

Kromayer96: Kromayer M, Wilting R, Tormay P, Bock A (1996). "Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB." J Mol Biol 262(4);413-20. PMID: 8893853

Kromayer99: Kromayer M, Neuhierl B, Friebel A, Bock A (1999). "Genetic probing of the interaction between the translation factor SelB and its mRNA binding element in Escherichia coli." Mol Gen Genet 262(4-5);800-6. PMID: 10628863

Leinfelder88a: 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

Li00b: Li C, Reches M, Engelberg-Kulka H (2000). "The bulged nucleotide in the Escherichia coli minimal selenocysteine insertion sequence participates in interaction with SelB: a genetic approach." J Bacteriol 182(22);6302-7. PMID: 11053373

Paleskava10: Paleskava A, Konevega AL, Rodnina MV (2010). "Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB." J Biol Chem 285(5);3014-20. PMID: 19940162

Ringquist94: Ringquist S, Schneider D, Gibson T, Baron C, Bock A, Gold L (1994). "Recognition of the mRNA selenocysteine insertion sequence by the specialized translational elongation factor SELB." Genes Dev 8(3);376-85. PMID: 8314089

Soler07: Soler N, Fourmy D, Yoshizawa S (2007). "Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB." J Mol Biol 370(4);728-41. PMID: 17537456

Stadtman91: Stadtman TC (1991). "Biosynthesis and function of selenocysteine-containing enzymes." J Biol Chem 266(25);16257-60. PMID: 1832153

Thanbichler00: Thanbichler M, Bock A, Goody RS (2000). "Kinetics of the interaction of translation factor SelB from Escherichia coli with guanosine nucleotides and selenocysteine insertion sequence RNA." J Biol Chem 275(27);20458-66. PMID: 10781605

Thanbichler01: Thanbichler M, Bock A (2001). "Functional analysis of prokaryotic SELB proteins." Biofactors 14(1-4);53-9. PMID: 11568440

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

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

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Wed Sep 2, 2015, biocyc14.