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Escherichia coli K-12 substr. MG1655 Enzyme: ornithine decarboxylase, degradative



Gene: speF Accession Numbers: EG10964 (EcoCyc), b0693, ECK0681

Regulation Summary Diagram: ?

Subunit composition of ornithine decarboxylase, degradative = [SpeF]2
         ornithine decarboxylase, degradative = SpeF

Summary:
E. coli encodes two ornithine decarboxylase enzymes, the biosynthetic (constitutive) SpeC and the degradative (inducible) SpeF [Tabor85, Kashiwagi91]. SpeF is activated by the guanosine nucleotides GTP, GDP, pppGpp and ppGpp [Kanjee11].

SpeF is overproduced from a speF-containing plasmid when cells are grown at pH 5.2, but not at pH 7 [Kashiwagi91]. Overexpression of RNase III from a plasmid increases expression from the speF promoter, perhaps by processing of the 5' UTR [Kashiwagi94].

Citations: [Gale40, Morris83, Shaibe85a, Soksawatmaekhin04, Kanjee12]

Locations: cytosol

Map Position: [717,485 <- 719,683] (15.46 centisomes)
Length: 2199 bp / 732 aa

Molecular Weight of Polypeptide: 82.416 kD (from nucleotide sequence), 80.0 kD (experimental) [Applebaum75 ]

Molecular Weight of Multimer: 160.0 kD (experimental) [Applebaum75]

pI: 5.88

Isozyme Sequence Similarity [Comment 1]:
ornithine decarboxylase, biosynthetic: YES

Unification Links: ASAP:ABE-0002362 , CGSC:31559 , DIP:DIP-154N , EchoBASE:EB0957 , EcoGene:EG10964 , EcoliWiki:b0693 , ModBase:P24169 , OU-Microarray:b0693 , PortEco:speF , PR:PRO_000023975 , Pride:P24169 , Protein Model Portal:P24169 , RefSeq:NP_415220 , RegulonDB:EG10964 , SMR:P24169 , String:511145.b0693 , UniProt:P24169

Relationship Links: InterPro:IN-FAMILY:IPR000310 , InterPro:IN-FAMILY:IPR005308 , InterPro:IN-FAMILY:IPR008286 , InterPro:IN-FAMILY:IPR011006 , InterPro:IN-FAMILY:IPR011193 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR027464 , InterPro:IN-FAMILY:IPR027568 , Pfam:IN-FAMILY:PF01276 , Pfam:IN-FAMILY:PF03709 , Pfam:IN-FAMILY:PF03711 , Prosite:IN-FAMILY:PS00703

In Paralogous Gene Group: 61 (5 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0001101 - response to acid chemical Inferred from experiment [Kashiwagi91]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01]
GO:0008295 - spermidine biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0033387 - putrescine biosynthetic process from ornithine Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004586 - ornithine decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Kanjee11]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01, Applebaum75]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for speF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Credits:
Last-Curated ? 14-May-2013 by Keseler I , SRI International


Enzymatic reaction of: ornithine decarboxylase

Synonyms: L-ornithine carboxy-lyase

EC Number: 4.1.1.17

L-ornithine + H+ <=> CO2 + putrescine

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.

In Pathways: superpathway of arginine and ornithine degradation , superpathway of ornithine degradation

Summary:
The enzyme was purified from E. coli UW44 [Applebaum75].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Applebaum75]

Activators (Unknown Mechanism): GTP [Kanjee11] , GDP [Kanjee11] , pppGpp [Kanjee11] , ppGpp [Kanjee11]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-ornithine
3600.0
[Applebaum75]

pH(opt) (forward direction): 7 [Applebaum75]

pH(opt): 6.9 [BRENDA14, Morris83], 8.3 [BRENDA14, Morris83]


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 355
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0693 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10964; confirmed by SwissProt match.


References

Applebaum75: Applebaum D, Sabo DL, Fischer EH, Morris DR (1975). "Biodegradative ornithine decarboxylase of Escherichia coli. Purification, properties, and pyridoxal 5'-phosphate binding site." Biochemistry 1975;14(16);3675-81. PMID: 240388

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

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

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

Gale40: Gale EF (1940). "The production of amines by bacteria: The decarboxylation of amino-acids by strains of Bacterium coli." Biochem J 34(3);392-413. PMID: 16747177

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.

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

Kanjee11: Kanjee U, Gutsche I, Ramachandran S, Houry WA (2011). "The Enzymatic Activities of the Escherichia coli Basic Aliphatic Amino Acid Decarboxylases Exhibit a pH Zone of Inhibition." Biochemistry 50(43);9388-98. PMID: 21957966

Kanjee12: Kanjee U, Ogata K, Houry WA (2012). "Direct binding targets of the stringent response alarmone (p)ppGpp." Mol Microbiol 85(6);1029-43. PMID: 22812515

Kashiwagi91: Kashiwagi K, Suzuki T, Suzuki F, Furuchi T, Kobayashi H, Igarashi K (1991). "Coexistence of the genes for putrescine transport protein and ornithine decarboxylase at 16 min on Escherichia coli chromosome." J Biol Chem 1991;266(31);20922-7. PMID: 1939141

Kashiwagi94: Kashiwagi K, Watanabe R, Igarashi K (1994). "Involvement of ribonuclease III in the enhancement of expression of the speF-potE operon encoding inducible ornithine decarboxylase and polyamine transport protein." Biochem Biophys Res Commun 200(1);591-7. PMID: 8166735

Morris83: Morris DR, Boeker EA (1983). "Biosynthetic and biodegradative ornithine and arginine decarboxylases from Escherichia coli." Methods Enzymol 1983;94;125-34. PMID: 6353148

Shaibe85a: Shaibe E, Metzer E, Halpern YS (1985). "Control of utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12." J Bacteriol 163(3);938-42. PMID: 3897202

Soksawatmaekhin04: Soksawatmaekhin W, Kuraishi A, Sakata K, Kashiwagi K, Igarashi K (2004). "Excretion and uptake of cadaverine by CadB and its physiological functions in Escherichia coli." Mol Microbiol 51(5);1401-12. PMID: 14982633

Stim93: Stim KP, Bennett GN (1993). "Nucleotide sequence of the adi gene, which encodes the biodegradative acid-induced arginine decarboxylase of Escherichia coli." J Bacteriol 1993;175(5);1221-34. PMID: 8383109

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: 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."


Report Errors or Provide Feedback
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 18.5 on Fri Dec 19, 2014, BIOCYC14B.