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

Gene: speE Accession Numbers: EG10963 (EcoCyc), b0121, ECK0120

Regulation Summary Diagram: ?

Regulation summary diagram for speE

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 [Zhou10]. Further site-directed mutagenesis confirmed the importance for catalysis of hydrophobic interactions contributed by residues in the gatekeeping loop [Lee12b].

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 [Lee12b].

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]

Locations: cytosol

Map Position: [135,598 <- 136,464] (2.92 centisomes, 11°)
Length: 867 bp / 288 aa

Molecular Weight of Polypeptide: 32.321 kD (from nucleotide sequence), 32.0 kD (experimental) [Lee12b ]

pI: 5.65

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

Relationship Links: InterPro:IN-FAMILY:IPR001045 , InterPro:IN-FAMILY:IPR029063 , InterPro:IN-FAMILY:IPR030373 , InterPro:IN-FAMILY:IPR030374 , Panther:IN-FAMILY:PTHR11558 , PDB:Structure:3O4F , Pfam:IN-FAMILY:PF01564 , Prosite:IN-FAMILY:PS01330 , Prosite:IN-FAMILY:PS51006

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0008295 - spermidine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, Tabor86]
GO:0006596 - polyamine biosynthetic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004766 - spermidine synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Lee12b, Tabor86]
GO:0010487 - thermospermine synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Bowman73]
GO:0042803 - protein homodimerization activity Inferred from experiment [Zhou10]
GO:0043918 - cadaverine aminopropyltransferase activity Inferred from experiment [Bowman73]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016768 - spermine synthase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: metabolism central intermediary metabolism polyamine biosynthesis

Essentiality data for speE 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]

Curated 11-Apr-2011 by Fulcher C , SRI International
Last-Curated ? 03-Oct-2012 by Keseler I , SRI International

Enzymatic reaction of: spermidine synthase

Synonyms: putrescine aminopropyltransferase, aminopropyltransferase, S-adenosylmethioninamine:putrescine 3-aminopropyltransferase

EC Number:

putrescine + S-adenosyl 3-(methylthio)propylamine <=> spermidine + S-methyl-5'-thioadenosine + H+

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]

Alternative Substrates for putrescine: spermidine [Bowman73 ]

In Pathways: superpathway of arginine and polyamine biosynthesis , superpathway of polyamine biosynthesis I , spermidine biosynthesis I

Purification of the enzyme was initially reported from E. coli W [Bowman73, Zappia80].

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 [Pegg83a].

Inhibitors (Unknown Mechanism): dicyclohexylamine [Tabor85, Pegg83a] , S-adenosyl-1,8-diamino-3-thiooctane [Tabor85, Pegg83a, Pegg86] , N-ethylmaleimide [Bowman73] , spermidine [Bowman73, Comment 5] , p-hydroxymercuribenzoate [Bowman73]

Kinetic Parameters:

Km (μM)
Vmax (µmol mg-1 min-1)
S-adenosyl 3-(methylthio)propylamine

T(opt): 50 °C [Lee12b]

pH(opt): 7.5 [Lee12b]

Enzymatic reaction of: aminopropylcadaverine synthase (spermidine synthase)

Synonyms: cadaverine aminopropyltransferase, aminopropyltransferase, S-adenosylmethioninamine:cadaverine 3-aminopropyltransferase

EC Number: 2.5.1.-

cadaverine + S-adenosyl 3-(methylthio)propylamine <=> aminopropylcadaverine + S-methyl-5'-thioadenosine + 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 favored in the direction shown.

In Pathways: superpathway of arginine and polyamine biosynthesis , superpathway of polyamine biosynthesis I , aminopropylcadaverine biosynthesis

The enzyme from E. coli W was shown to use cadaverine as a substrate, but at a reduced rate relative to putrescine [Bowman73].

Sequence Features

Protein sequence of SpeE with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Tabor86, UniProt11]
UniProt: Removed.
Chain 2 -> 288
UniProt: Spermidine synthase;
Amino-Acid-Sites-That-Bind 9
UniProt: Polyamine.
Conserved-Region 9 -> 238
UniProt: PABS.
Amino-Acid-Sites-That-Bind 33
UniProt: S-adenosylmethioninamine; Non-Experimental Qualifier: by similarity;
Protein-Segment 53 -> 54
UniProt: Polyamine binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 64
UniProt: Polyamine.
Amino-Acid-Sites-That-Bind 88
UniProt: S-adenosylmethioninamine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 108
UniProt: S-adenosylmethioninamine; Non-Experimental Qualifier: by similarity;
Protein-Segment 140 -> 141
UniProt: S-adenosylmethioninamine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Active-Site 158
[Lee12b, UniProt15]
UniProt: Proton acceptor.
Mutagenesis-Variant 158
[Lee12b, UniProt14a]
UniProt: Completely inactive.
Mutagenesis-Variant 159
[Lee12b, UniProt14a]
[Lee12b, UniProt14a]
C → S: No influence on aminopropyltransferase activity.
C → A: Reduction of 23% of the aminopropyltransferase activity.
Protein-Segment 159 -> 161
UniProt: Polyamine binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 160
[Lee12b, UniProt14a]
UniProt: Reduction of aminopropyltransferase activity.
Mutagenesis-Variant 161
[Lee12b, UniProt14a]
UniProt: Completely inactive.
Mutagenesis-Variant 162
[Lee12b, UniProt14a]
UniProt: No influence on aminopropyltransferase activity.
Mutagenesis-Variant 163
[Lee12b, UniProt14a]
UniProt: No influence on aminopropyltransferase activity.
Amino-Acid-Sites-That-Bind 165
UniProt: S-adenosylmethioninamine; via carbonyl oxygen.
Mutagenesis-Variant 165
[Lee12b, UniProt14a]
UniProt: Reduction of aminopropyltransferase activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0121 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10963; 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

Bowman73: Bowman WH, Tabor CW, Tabor H (1973). "Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli." J Biol Chem 1973;248(7);2480-6. PMID: 4572733

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

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

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

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

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

Lee12b: Lee MJ, Yang YT, Lin V, Huang H (2012). "Site-Directed Mutations of the Gatekeeping Loop Region Affect the Activity of Escherichia coli Spermidine Synthase." Mol Biotechnol. PMID: 23001854

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

Minton90: Minton KW, Tabor H, Tabor CW (1990). "Paraquat toxicity is increased in Escherichia coli defective in the synthesis of polyamines." Proc Natl Acad Sci U S A 87(7);2851-5. PMID: 2181453

Pegg83a: 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

Pegg86: 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

Tabor83a: Tabor CW, Tabor H (1983). "Putrescine aminopropyltransferase (Escherichia coli)." Methods Enzymol 1983;94;265-70. PMID: 6312268

Tabor85: Tabor CW, Tabor H (1985). "Polyamines in microorganisms." Microbiol Rev 1985;49(1);81-99. PMID: 3157043

Tabor86: Tabor CW, Tabor H, Xie QW (1986). "Spermidine synthase of Escherichia coli: localization of the speE gene." Proc Natl Acad Sci U S A 83(16);6040-4. PMID: 3526348

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 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 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."

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

Xie89: Xie QW, Tabor CW, Tabor H (1989). "Spermidine biosynthesis in Escherichia coli: promoter and termination regions of the speED operon." J Bacteriol 1989;171(8);4457-65. PMID: 2666401

Xie93: Xie QW, Tabor CW, Tabor H (1993). "Deletion mutations in the speED operon: spermidine is not essential for the growth of Escherichia coli." Gene 1993;126(1);115-7. PMID: 8472951

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

Zhou10: 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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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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