Escherichia coli K-12 substr. MG1655 Enzyme: lysine decarboxylase 2

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

Synonyms: ldc, ldcH, LDC2

Regulation Summary Diagram: ?

Regulation summary diagram for ldcC

Subunit composition of lysine decarboxylase 2 = [LdcC]10

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, Yamamoto97, Kikuchi97, 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 [Kanjee11a].

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" [Yamamoto97]

Locations: cytosol

Map Position: [209,679 -> 211,820] (4.52 centisomes, 16°)
Length: 2142 bp / 713 aa

Molecular Weight of Polypeptide: 80.59 kD (from nucleotide sequence), 80.0 kD (experimental) [Kikuchi97 ]

Molecular Weight of Multimer: 800.0 kD (experimental) [Kikuchi97]

Isozyme Sequence Similarity:

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

In Paralogous Gene Group: 61 (5 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006554 - lysine catabolic process Inferred from experiment [Kikuchi97]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0008923 - lysine decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01, Kikuchi97]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for ldcC 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 ? 11-Nov-2011 by Keseler I , SRI International

Enzymatic reaction of: lysine decarboxylase

Synonyms: L-lysine carboxy-lyase

EC Number:

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 , L-lysine degradation I , aminopropylcadaverine biosynthesis

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Kikuchi97]

Inhibitors (Unknown Mechanism): ppGpp [Kanjee11a] , pppGpp [Kanjee11a] , putrescine [Wertheimer83, Yamamoto97] , spermidine [Wertheimer83]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Specific Activity (U/mg)
[Boeker83, BRENDA14]
[Vienozinskiene85, BRENDA14]
[Kanjee11, BRENDA14]

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

pH(opt): 5.7 [BRENDA14, Vienozinskiene85], 6.2 [BRENDA14, Kikuchi97], 7.6 [Lemonnier98]

Sequence Features

Protein sequence of LdcC with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 284
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 314
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);
N6-pyridoxal-phosphate-Lys-Modification 367
UniProt: N6-(pyridoxal phosphate)lysine.
Sequence-Conflict 411
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 413 -> 414
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 498
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);
Sequence-Conflict 673
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2; AA sequence);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

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."

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

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."

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

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, 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

Kanjee11a: 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

Kikuchi97: 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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

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

Yamamoto97: 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

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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 Wed Oct 7, 2015, BIOCYC14A.