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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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MetaCyc Enzyme: lysine decarboxylase 2

Gene: ldcC Accession Numbers: G6094 (MetaCyc), b0186, ECK0185

Synonyms: ldc, ldcH, LDC2

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of lysine decarboxylase 2 = [LdcC]10

Summary:
There are two lysine decarboxylases in E. coli, encoded by the cadA and ldcC genes. The ldcC gene product, lysine decarboxylase 2 (LDC2), differs from the cadA-encoded enzyme, LDC, in that it is weakly expressed, is more thermosensitive and has activity over a broad range of pH with a higher pH optimum than LDC [Goldemberg80, Wertheimer83, Yamamoto97a, Kikuchi97a, Lemonnier98].

ldcC is expressed at very low levels [Lemonnier98] and shows RpoS-dependent induction during stationary phase [Kikuchi98, Schellhorn98]. The alarmone (p)ppGpp inhibits LdcC activity [Kanjee11].

A mutant that is missing all eight genes involved in polyamine biosynthesis, ΔspeABCDEF cadA ldcC, grows aerobically at a reduced rate. However, polyamines are required for growth under anaerobic conditions and at very high oxygen levels [Chattopadhyay09].

LdcC: "lysine decarboxylase, constitutive" [Yamamoto97a]

Locations: cytosol

Map Position: [209,679 -> 211,820]

Molecular Weight of Polypeptide: 80.59 kD (from nucleotide sequence), 80.0 kD (experimental) [Kikuchi97a ]

Molecular Weight of Multimer: 800.0 kD (experimental) [Kikuchi97a]

Unification Links: ASAP:ABE-0000633 , DIP:DIP-10086N , EchoBASE:EB3010 , EcoGene:EG13219 , EcoliWiki:b0186 , Mint:MINT-1275881 , ModBase:P52095 , OU-Microarray:b0186 , PortEco:ldcC , PR:PRO_000023075 , Protein Model Portal:P52095 , RefSeq:NP_414728 , RegulonDB:G6094 , SMR:P52095 , String:511145.b0186 , UniProt:P52095

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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006554 - lysine catabolic process Inferred from experiment [Kikuchi97a]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0008923 - lysine decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01a, Kikuchi97a]
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]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: lysine decarboxylase

Synonyms: L-lysine carboxy-lyase

EC Number: 4.1.1.18

L-lysine + H+ <=> CO2 + cadaverine

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 polyamine biosynthesis , superpathway of polyamine biosynthesis I , superpathway of lysine degradation , aminopropylcadaverine biosynthesis , lysine degradation I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Kikuchi97a]

Inhibitors (Unknown Mechanism): ppGpp [Kanjee11] , pppGpp [Kanjee11] , putrescine [Wertheimer83, Yamamoto97a] , spermidine [Wertheimer83]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Specific Activity (U/mg)
Citations
L-lysine
1500.0
[Boeker83, BRENDA14]
L-lysine
2000.0
[Vienozinskiene85, BRENDA14]
L-lysine
420.0
30.0
[Kanjee11a, BRENDA14]
L-lysine
[Kikuchi97a]

T(opt): 60 °C [BRENDA14, Vienozinskiene85], 52 °C [Lemonnier98]

pH(opt): 5.7 [BRENDA14, Vienozinskiene85], 6.2 [BRENDA14, Kikuchi97a], 7.6 [Lemonnier98]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 284
[Yamamoto97a, UniProt10]
Alternate sequence: T; UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 314
[Yamamoto97a, UniProt10]
Alternate sequence: F; UniProt: (in Ref. 2; AA sequence);
N6-pyridoxal-phosphate-Lys-Modification 367
[UniProt11]
UniProt: N6-(pyridoxal phosphate)lysine.
Sequence-Conflict 411
[Yamamoto97a, UniProt10]
Alternate sequence: S; UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 413 -> 414
[Yamamoto97a, UniProt10]
Alternate sequence: R; UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 498
[Yamamoto97a, UniProt10]
Alternate sequence: I; UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 673
[Yamamoto97a, UniProt10]
Alternate sequence: I; UniProt: (in Ref. 2; AA sequence);

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Boeker83: Boeker EA, Fischer EH (1983). "Lysine decarboxylase (Escherichia coli B)." Methods Enzymol 94;180-4. PMID: 6353151

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chattopadhyay09: Chattopadhyay MK, Tabor CW, Tabor H (2009). "Polyamines are not required for aerobic growth of Escherichia coli: preparation of a strain with deletions in all of the genes for polyamine biosynthesis." J Bacteriol 191(17);5549-52. PMID: 19542271

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

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.

Goldemberg80: Goldemberg SH (1980). "Lysine decarboxylase mutants of Escherichia coli: evidence for two enzyme forms." J Bacteriol 141(3);1428-31. PMID: 6767710

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

Kanjee11a: Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA (2011). "Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase." EMBO J 30(5);931-44. PMID: 21278708

Kikuchi97a: Kikuchi Y, Kojima H, Tanaka T, Takatsuka Y, Kamio Y (1997). "Characterization of a second lysine decarboxylase isolated from Escherichia coli." J Bacteriol 1997;179(14);4486-92. PMID: 9226257

Kikuchi98: Kikuchi Y, Kurahashi O, Nagano T, Kamio Y (1998). "RpoS-dependent expression of the second lysine decarboxylase gene in Escherichia coli." Biosci Biotechnol Biochem 62(6);1267-70. PMID: 9692215

Lemonnier98: Lemonnier M, Lane D (1998). "Expression of the second lysine decarboxylase gene of Escherichia coli." Microbiology 1998;144 ( Pt 3);751-60. PMID: 9534244

Schellhorn98: Schellhorn HE, Audia JP, Wei LI, Chang L (1998). "Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli." J Bacteriol 180(23);6283-91. PMID: 9829938

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: 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."

Vienozinskiene85: Vienozinskiene J, Januseviciute R, Pauliukonis A, Kazlauskas D (1985). "Lysine decarboxylase assay by the pH-stat method." Anal Biochem 146(1);180-3. PMID: 3887985

Wertheimer83: Wertheimer SJ, Leifer Z (1983). "Putrescine and spermidine sensitivity of lysine decarboxylase in Escherichia coli: evidence for a constitutive enzyme and its mode of regulation." Biochem Biophys Res Commun 114(2);882-8. PMID: 6349639

Yamamoto97a: Yamamoto Y, Miwa Y, Miyoshi K, Furuyama J, Ohmori H (1997). "The Escherichia coli ldcC gene encodes another lysine decarboxylase, probably a constitutive enzyme." Genes Genet Syst 1997;72(3);167-72. PMID: 9339543


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, BIOCYC13A.