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MetaCyc Enzyme: selenide, water dikinase

Gene: selD Accession Numbers: EG10943 (MetaCyc), b1764, ECK1762

Synonyms: fdhB

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of selenide, water dikinase = [SelD]2
         selenide, water dikinase = SelD

Summary:
Selenide, water dikinase (SelD) catalyzes the reaction that produces selenophosphate, the selenium donor for the biosynthesis of selenocysteine and modification of thiouridine to selenouridine in certain tRNAs [Ehrenreich92].

The enzyme is a dimer in solution and a crystal structure, with a Kd of 170 nM [Noinaj12]. The Cys17 [Kim92, Kim93], Lys20 [Kim93], and Asn87 [Noinaj12] residues are essential for SelD catalytic activity. A crystal structure of the C17S mutant enzyme has been solved, showing a set of conserved aspartate residues that are involved in Mg2+ binding and are required for catalytic activity. A reaction mechanism has been proposed [Noinaj12]. SelD contains an unidentified chromophore [Wolfe03a].

The CsdA, CsdB and IscS proteins can all provide the selenium needed for the reaction [Lacourciere00]. E. coli can utilize external selenocysteine as a source of selenium for biosynthesis of selenophosphate [Lacourciere02].

A selD mutant is defective in both selenocysteine incorporation and seleno-modification of tRNA [Leinfelder90, Leinfelder88a].

Reviews: [Lacourciere99a, Lacourciere01, Wolfe04b]

Citations: [Haddock82]

Locations: cytosol

Map Position: [1,844,989 <- 1,846,032]

Molecular Weight of Polypeptide: 36.687 kD (from nucleotide sequence), 36.0 kD (experimental) [Leinfelder90 ]

Unification Links: ASAP:ABE-0005872 , CGSC:32292 , DIP:DIP-10849N , EchoBASE:EB0936 , EcoGene:EG10943 , EcoliWiki:b1764 , Mint:MINT-1256873 , ModBase:P16456 , OU-Microarray:b1764 , PortEco:selD , PR:PRO_000023932 , Pride:P16456 , Protein Model Portal:P16456 , RefSeq:NP_416278 , RegulonDB:EG10943 , SMR:P16456 , String:511145.b1764 , UniProt:P16456

Relationship Links: InterPro:IN-FAMILY:IPR000728 , InterPro:IN-FAMILY:IPR004536 , InterPro:IN-FAMILY:IPR010918 , InterPro:IN-FAMILY:IPR016188 , InterPro:IN-FAMILY:IPR023061 , PDB:Structure:3U0O , Pfam:IN-FAMILY:PF00586 , Pfam:IN-FAMILY:PF02769

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0016260 - selenocysteine biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Leinfelder88a, Leinfelder90]
GO:0070329 - tRNA seleno-modification Inferred from experiment [Leinfelder90, Leinfelder88a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, Noinaj12]
GO:0004756 - selenide, water dikinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Ehrenreich92]
GO:0042803 - protein homodimerization activity Inferred from experiment [Noinaj12]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by curator

MultiFun Terms: information transfer protein related amino acid -activation
information transfer RNA related RNA modification

Credits:
Created in EcoCyc 21-Nov-2011 by Keseler I , SRI International
Imported from EcoCyc 27-Jan-2015 by Paley S , SRI International


Enzymatic reaction of: selenide, water dikinase

Synonyms: selenophosphate synthetase, selenium donor protein

EC Number: 2.7.9.3

selenide + ATP + H2O <=> selenophosphate + AMP + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown. [Veres94]

In Pathways: L-selenocysteine biosynthesis I (bacteria)

Credits:
Imported from EcoCyc 27-Jan-2015 by Paley S , SRI International

Cofactors or Prosthetic Groups: K+ [Veres94], Mg2+ [Comment 1, Kim93]

Inhibitors (Competitive): AMP (Kic = 170µM) [Veres94, Comment 2]

Inhibitors (Unknown Mechanism): Zn2+ [Veres94, Kim93, Kim94]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
1600.0
[Preabrazhenskay09, BRENDA14]
ATP
900.0
[Veres94, BRENDA14]
ATP
900.0
[Lacourciere99, BRENDA14]
ATP
900.0
[Kim93, BRENDA14]
selenide
20.0
[Lacourciere99, BRENDA14]

T(opt): 37 °C [BRENDA14, Preabrazhenskay09]

pH(opt): 7.2 [BRENDA14, Veres94], 8 [BRENDA14, Preabrazhenskay09]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 13
[UniProt10a]
UniProt: No loss of activity;
Mutagenesis-Variant 17
[Kim92, UniProt11]
UniProt: Complete loss of activity.
Active-Site 17
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Mutagenesis-Variant 18
[UniProt10a]
UniProt: Partial loss of activity;
Mutagenesis-Variant 19
[Kim92, UniProt11]
UniProt: No loss of activity.
Mutagenesis-Variant 20
[UniProt10a]
[UniProt10a]
Q: Complete loss of activity;
R: Marked loss of activity;
Amino-Acid-Site 20
[UniProt10a]
UniProt: Important for catalytic activity; Sequence Annotation Type: site;
Nucleotide-Phosphate-Binding-Region 230 -> 236
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;

History:
10/20/97 Gene b1764 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10943; confirmed by SwissProt match.


References

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

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

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."

Haddock82: Haddock BA, Mandrand-Berthelot MA (1982). "Escherichia coli formate-to-nitrate respiratory chain: genetic analysis." Biochem Soc Trans 10(6);478-80. PMID: 6759194

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Lacourciere00: Lacourciere GM, Mihara H, Kurihara T, Esaki N, Stadtman TC (2000). "Escherichia coli NifS-like proteins provide selenium in the pathway for the biosynthesis of selenophosphate." J Biol Chem 2000;275(31);23769-73. PMID: 10829016

Lacourciere01: Lacourciere GM, Stadtman TC (2001). "Utilization of selenocysteine as a source of selenium for selenophosphate biosynthesis." Biofactors 14(1-4);69-74. PMID: 11568442

Lacourciere02: Lacourciere GM (2002). "Selenium is mobilized in vivo from free selenocysteine and is incorporated specifically into formate dehydrogenase H and tRNA nucleosides." J Bacteriol 184(7);1940-6. PMID: 11889101

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

Lacourciere99a: Lacourciere GM (1999). "Biosynthesis of selenophosphate." Biofactors 10(2-3);237-44. PMID: 10609888

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

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

Liu97: 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

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

Noinaj12: Noinaj N, Wattanasak R, Lee DY, Wally JL, Piszczek G, Chock PB, Stadtman TC, Buchanan SK (2012). "Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase." J Bacteriol 194(2);499-508. PMID: 22081394

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

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

UniProt10a: 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.

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

Veres94: Veres Z, Kim IY, Scholz TD, Stadtman TC (1994). "Selenophosphate synthetase. Enzyme properties and catalytic reaction." J Biol Chem 269(14);10597-603. PMID: 8144648

Veres94a: Veres, Z, Kim, IY, Scholz, TD, Stadtman, TC "Selenophosphate synthetase Enzyme properties and catalytic reaction." The Journal of Biological Chemistry 269:10597-10603 (1994).

Walker98: Walker H, Ferretti JA, Stadtman TC (1998). "Isotope exchange studies on the Escherichia coli selenophosphate synthetase mechanism." Proc Natl Acad Sci U S A 1998;95(5);2180-5. PMID: 9482859

Wolfe03a: Wolfe MD (2003). "Mechanistic insights revealed through characterization of a novel chromophore in selenophosphate synthetase from Escherichia coli." IUBMB Life 55(12);689-93. PMID: 14769005

Wolfe04b: Wolfe MD (2004). "Selenophosphate Synthetase." EcoSal Online, module 3.6.1.1.2.


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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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