Escherichia coli K-12 substr. MG1655 Enzyme: agmatinase

Gene: speB Accession Numbers: EG10960 (EcoCyc), b2937, ECK2932

Regulation Summary Diagram: ?

Regulation summary diagram for speB

Subunit composition of agmatinase = [SpeB]2

Agmatinase (SpeB) carries out the second step in putrescine biosynthesis, generating the pathway's putrescine product.

SpeB catalyzes the hydrolysis of agmatine to yield urea and putrescine [Hafner77, Satishchandran84, Boyle84, Satishchandran90].

Agmatinase comprises a dimer of SpeB monomers [Satishchandran86]. One molecule of Mn2+ is present per SpeB monomer [Carvajal99].

SpeB is not subject to inhibition by putrescine in the manner of its immediate upstream enzyme SpeA. However, agmatinase activity is downregulated in a dose- and CRP-dependent fashion by cAMP, and is induced by the presence of its substrate, agmatine. Both responses depend on protein synthesis, indicating they occur via modulation of protein level rather than enzyme activity [Satishchandran84].

Gene Citations: [Szumanski90]

Locations: cytosol

Map Position: [3,080,899 <- 3,081,819] (66.4 centisomes, 239°)
Length: 921 bp / 306 aa

Molecular Weight of Polypeptide: 33.557 kD (from nucleotide sequence), 38.0 kD (experimental) [Satishchandran86 ]

Molecular Weight of Multimer: 80.0 kD (experimental) [Satishchandran86]

pI: 5.44

Unification Links: ASAP:ABE-0009632 , CGSC:160 , DIP:DIP-10906N , EchoBASE:EB0953 , EcoGene:EG10960 , EcoliWiki:b2937 , ModBase:P60651 , OU-Microarray:b2937 , PortEco:speB , PR:PRO_000023972 , Pride:P60651 , Protein Model Portal:P60651 , RefSeq:NP_417412 , RegulonDB:EG10960 , SMR:P60651 , String:511145.b2937 , Swiss-Model:P60651 , UniProt:P60651

Relationship Links: InterPro:IN-FAMILY:IPR005925 , InterPro:IN-FAMILY:IPR006035 , InterPro:IN-FAMILY:IPR020855 , InterPro:IN-FAMILY:IPR023694 , InterPro:IN-FAMILY:IPR023696 , Panther:IN-FAMILY:PTHR11358 , Pfam:IN-FAMILY:PF00491 , Prosite:IN-FAMILY:PS01053 , Prosite:IN-FAMILY:PS51409

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for speB

GO Terms:

Biological Process: GO:0009446 - putrescine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Satishchandran86]
GO:0006596 - polyamine biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0008295 - spermidine biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0033388 - putrescine biosynthetic process from arginine Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0008783 - agmatinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Satishchandran86]
GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Carvajal99]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016813 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism central intermediary metabolism polyamine biosynthesis

Essentiality data for speB 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 ? 18-Nov-2008 by Shearer A , SRI International

Enzymatic reaction of: agmatinase

Synonyms: agmatine ureohydrolase, AUH, agmatine amidinohydrolase

EC Number:

agmatine + H2O <=> urea + putrescine

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: superpathway of L-arginine and L-ornithine degradation , superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation , superpathway of arginine and polyamine biosynthesis , superpathway of polyamine biosynthesis I , L-arginine degradation III (arginine decarboxylase/agmatinase pathway) , putrescine biosynthesis I

The Ki values for ornithine and arginine are 6 mM and 9 mM, respectively [Satishchandran86].

The Km for agmatine is a slightly different 1.9 mM when assayed by an alternate colorimetric method [Satishchandran86].

Cofactors or Prosthetic Groups: Mn2+ [Satishchandran86]

Inhibitors (Competitive): L-arginine [Satishchandran86]

Inhibitors (Noncompetitive): L-ornithine [Satishchandran86]

Inhibitors (Unknown Mechanism): EDTA [Satishchandran86] , EGTA [Satishchandran86]

Kinetic Parameters:

Km (μM)
[Carvajal04, BRENDA14]
[Satishchandran86, BRENDA14]

T(opt): 42 °C [BRENDA14, Satishchandran86]

pH(opt): 7.3 [Satishchandran86]

Sequence Features

Protein sequence of SpeB with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 126
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Active-Site 126, 151, 153, 163
[Carvajal99a, Salas02, Salas04]
These residues are all involved in activity or substrate binding.
Metal-Binding-Site 149
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 151
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 153
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 163
UniProt: Important for catalytic activity; Sequence Annotation Type: site.
Mutagenesis-Variant 163
[Carvajal99a, UniProt14]
UniProt: Loss of activity.
Metal-Binding-Site 230
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 232
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2937 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10960; 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

Boyle84: Boyle SM, Markham GD, Hafner EW, Wright JM, Tabor H, Tabor CW (1984). "Expression of the cloned genes encoding the putrescine biosynthetic enzymes and methionine adenosyltransferase of Escherichia coli (speA, speB, speC and metK)." Gene 30(1-3);129-36. PMID: 6392022

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

Carvajal04: Carvajal N, Orellana MS, Salas M, Enriquez P, Alarcon R, Uribe E, Lopez V (2004). "Kinetic studies and site-directed mutagenesis of Escherichia coli agmatinase. A role for Glu274 in binding and correct positioning of the substrate guanidinium group." Arch Biochem Biophys 430(2);185-90. PMID: 15369817

Carvajal99: Carvajal N, Lopez V, Salas M, Uribe E, Herrera P, Cerpa J (1999). "Manganese is essential for catalytic activity of Escherichia coli agmatinase." Biochem Biophys Res Commun 258(3);808-11. PMID: 10329468

Carvajal99a: Carvajal N, Olate J, Salas M, Lopez V, Cerpa J, Herrera P, Uribe E (1999). "Evidence that histidine-163 is critical for catalytic activity, but not for substrate binding to Escherichia coli agmatinase." Biochem Biophys Res Commun 264(1);196-200. PMID: 10527864

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, 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."

Hafner77: Hafner EW, Tabor CW, Tabor H (1977). "Isolation of a metK mutant with a temperature-sensitive S-adenosylmethionine synthetase." J Bacteriol 132(3);832-40. PMID: 336609

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

Salas02: Salas M, Rodriguez R, Lopez N, Uribe E, Lopez V, Carvajal N (2002). "Insights into the reaction mechanism of Escherichia coli agmatinase by site-directed mutagenesis and molecular modelling." Eur J Biochem 269(22);5522-6. PMID: 12423350

Salas04: Salas M, Lopez V, Uribe E, Carvajal N (2004). "Studies on the interaction of Escherichia coli agmatinase with manganese ions: structural and kinetic studies of the H126N and H151N variants." J Inorg Biochem 98(6);1032-6. PMID: 15149812

Satishchandran84: Satishchandran C, Boyle SM (1984). "Antagonistic transcriptional regulation of the putrescine biosynthetic enzyme agmatine ureohydrolase by cyclic AMP and agmatine in Escherichia coli." J Bacteriol 157(2);552-9. PMID: 6319366

Satishchandran86: Satishchandran C, Boyle SM (1986). "Purification and properties of agmatine ureohydrolyase, a putrescine biosynthetic enzyme in Escherichia coli." J Bacteriol 1986;165(3);843-8. PMID: 3081491

Satishchandran90: Satishchandran C, Markham GD, Moore RC, Boyle SM (1990). "Locations of the speA, speB, speC, and metK genes on the physical map of Escherichia coli." J Bacteriol 172(9);4748. PMID: 2203728

Szumanski90: Szumanski MB, Boyle SM (1990). "Analysis and sequence of the speB gene encoding agmatine ureohydrolase, a putrescine biosynthetic enzyme in Escherichia coli." J Bacteriol 1990;172(2);538-47. PMID: 2153656

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

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

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

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."

Other References Related to Gene Regulation

He93: He B, Choi KY, Zalkin H (1993). "Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor." J Bacteriol 1993;175(11);3598-606. PMID: 8388874

Moore90: Moore RC, Boyle SM (1990). "Nucleotide sequence and analysis of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli." J Bacteriol 1990;172(8);4631-40. PMID: 2198270

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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 Sat Oct 10, 2015, biocyc13.