|Gene:||speE||Accession Numbers: EG10963 (EcoCyc), b0121, ECK0120|
Subunit composition of spermidine synthase = [SpeE]2
Spermidine synthase (SpeE) catalyzes the final step in the biosynthesis of the polyamine spermidine.
The crystal structure of SpeE has been determined at 2.9 Å resolution. The enzyme is a dimer both in solution and the crystal structure. Each SpeE monomer consists of two domains: a small N-terminal β-strand domain which includes 6 β-strands and a C-terminal catalytic core domain that adopts a canonical methyltransferase (MTase) fold. E. coli SpeE possesses a unique large substrate-binding pocket that is probably responsible for a broader substrate specificity of this enzyme, compared to its orthologs. Three aspartic acid residues, Asp88, Asp158, and Asp161 in SpeE play key roles in the aminopropyltransferase reaction. The carboxylate side chain of Asp158 plays a major role in the deprotonation of the substrate and is aided by Tyr63 and Tyr226 [Zhou10a]. Further site-directed mutagenesis confirmed the importance for catalysis of hydrophobic interactions contributed by residues in the gatekeeping loop [Lee12a].
The enzyme was first purified from E. coli W [Bowman73] and later subjected to kinetic analysis and substrate analog inhibition studies; a reaction mechanism was proposed [Zappia80]. Experiments with the E. coli K-12 enzyme also suggest a ping-pong reaction mechanism [Lee12a].
Only one enzyme with aminopropyltransferase activity has been found in E. coli [Tabor83a]. Inhibition of spermidine synthase activity by dicyclohexylamine inhibits growth of E. coli [Mattila84]. Strains lacking the ability to synthesize spermidine have near-normal growth rates [Xie93], but are more sensitive to paraquat than wild type [Minton90].
Gene Citations: [Xie89]
|Map Position: [135,598 <- 136,464] (2.92 centisomes)||Length: 867 bp / 288 aa|
Molecular Weight of Polypeptide: 32.321 kD (from nucleotide sequence), 32.0 kD (experimental) [Lee12a ]
Unification Links: ASAP:ABE-0000418 , CGSC:17590 , DIP:DIP-10908N , EchoBASE:EB0956 , EcoGene:EG10963 , EcoliWiki:b0121 , Entrez-gene:947726 , Mint:MINT-1231846 , ModBase:P09158 , OU-Microarray:b0121 , PortEco:speE , Pride:P09158 , Protein Model Portal:P09158 , RefSeq:NP_414663 , RegulonDB:EG10963 , SMR:P09158 , String:511145.b0121 , UniProt:P09158
|Biological Process:||GO:0008295 - spermidine biosynthetic process
[UniProtGOA12, UniProt-GOA, 2011, GOA06, Tabor86]
GO:0006596 - polyamine biosynthetic process [UniProt-GOA, 2011]
|Molecular Function:||GO:0004766 - spermidine synthase activity
[GOA06, GOA01, Lee12a, Tabor86]
GO:0042803 - protein homodimerization activity [Zhou10a]
GO:0003824 - catalytic activity [GOA et al., 2001]
GO:0016740 - transferase activity [UniProt-GOA, 2011]
|Cellular Component:||GO:0005829 - cytosol
[Diaz-Mejia et al., 2009, Ishihama et al., 2008, LopezCampistrou05, Lasserre06]
GO:0005737 - cytoplasm [UniProtGOA11, UniProt-GOA, 2011]
|MultiFun Terms:||metabolism → central intermediary metabolism → polyamine biosynthesis|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB enriched||Yes||37||Aerobic||6.95||Yes [Gerdes et al., 2003, Comment 1]|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba et al., 2006, Comment 2]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce et al., 2006, Comment 3]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba et al., 2006, Comment 2] |
Yes [Feist07, Comment 4]
Enzymatic reaction of: spermidine synthase
Synonyms: putrescine aminopropyltransferase, aminopropyltransferase, S-adenosylmethioninamine:putrescine 3-aminopropyltransferase
EC Number: 184.108.40.206
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 irreversible in the direction shown. [Bowman73]
Spermidine synthase activity was demonstrated after overexpression of plasmid-borne speE in a Δ(speE-speD) mutant [Tabor86].
Inhibition of this enzyme by S-adenosyl-1,8-diamino-3-thiooctane and dicyclohexylamine was studied in an Escherichia coli strain designated Merrell Research Center 59 [Pegg83].
Inhibitors (Unknown Mechanism): dicyclohexylamine [Tabor85, Pegg83] , S-adenosyl-1,8-diamino-3-thiooctane [Tabor85, Pegg83, Pegg86a] , N-ethylmaleimide [Bowman73] , spermidine [Bowman73, Comment 5] , p-hydroxymercuribenzoate [Bowman73]
T(opt): 50 °C [Lee12a]
pH(opt): 7.5 [Lee12a]
Enzymatic reaction of: aminopropylcadaverine synthase (spermidine synthase)
Synonyms: cadaverine aminopropyltransferase, aminopropyltransferase, S-adenosylmethioninamine:cadaverine 3-aminopropyltransferase
EC Number: 2.5.1.-
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 favored in the direction shown.
The enzyme from E. coli W was shown to use cadaverine as a substrate, but at a reduced rate relative to putrescine [Bowman73].
|Chain||2 -> 288|
|Conserved-Region||9 -> 238|
|Protein-Segment||140 -> 141|
10/20/97 Gene b0121 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10963; confirmed by SwissProt match.
Baba et al., 2006: 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
Diaz-Mejia et al., 2009: 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
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
Gerdes et al., 2003: 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
Ishihama et al., 2008: 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
Joyce et al., 2006: 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
Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726
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
Mattila84: Mattila T, Honkanen-Buzalski T, Poso H (1984). "Reversible inhibition of bacterial growth after specific inhibition of spermidine synthase by dicyclohexylamine." Biochem J 223(3);823-30. PMID: 6508744
Pegg83: Pegg AE, Bitonti AJ, McCann PP, Coward JK (1983). "Inhibition of bacterial aminopropyltransferases by S-adenosyl-1,8-diamino-3-thiooctane and by dicyclohexylamine." FEBS Lett 155(2);192-6. PMID: 6406265
Pegg86a: Pegg AE, Coward JK, Talekar RR, Secrist JA (1986). "Effects of certain 5'-substituted adenosines on polyamine synthesis: selective inhibitors of spermine synthase." Biochemistry 1986;25(14);4091-7. PMID: 3091070
Zappia80: Zappia V, Cacciapuoti G, Pontoni G, Oliva A (1980). "Mechanism of propylamine-transfer reactions. Kinetic and inhibition studies on spermidine synthase from Escherichia coli." J Biol Chem 255(15);7276-80. PMID: 6993485
Zhou10a: Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J (2010). "The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket." J Struct Biol 169(3);277-85. PMID: 20051267
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