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Escherichia coli K-12 substr. MG1655 Enzyme: lysine decarboxylase 1



Gene: cadA Accession Numbers: EG10131 (EcoCyc), b4131, ECK4125

Regulation Summary Diagram: ?

Subunit composition of lysine decarboxylase 1 = [CadA]10

Summary:
There are two lysine decarboxylases in E. coli, encoded by the cadA and ldcC genes. The cadA gene product, lysine decarboxylase 1 (LDC1), is more active, is thermostable, and has a lower pH optimum than the ldcC-encoded enzyme, LDC2 [Goldemberg80]. [Lemonnier98, Yamamoto97, Kikuchi97a]

LDC1 is part of the lysine-dependent acid resistance system 4 (AR4) which confers resistance to weak organic acids produced during carbohydrate fermentation under conditions of anaerobiosis and phosphate starvation. Lysine decarboxylase is a biodegradative enzyme. It is induced under acidic pH conditions and plays a role in maintaining pH homeostasis or extending the growth period by detoxification of the extracellular medium. The CO2 produced by CadA may be physiologically important when the TCA cycle is down-regulated under conditions of anaerobiosis and low pH, and CO2 production is therefore reduced [Takayama94].

Lysine provides protection during anaerobic phosphate starvation, dramatically increasing viability, and a cadBA deletion completely reverses this effect [Moreau07]. Overproduction of CadA affects the growth rate [Mandic98]. A speA speB speC speD cadA quintuple mutant is viable, albeit slow growing, on media deficient in amines, indicating that polyamines are not required for growth [Tabor80].

LDC1 interacts with and stimulates the ATPase activity of RavA [Snider06]. Interaction with RavA reduces the inhibitory effect of the alarmone ppGpp on LDC1 activity [El10].

LDC1 production is induced under anaerobic growth conditions and acid pH [Goldemberg80]. Regulation has been described [Auger89, Meng92a, Shi93, Takayama94, Neely94, Dell94, Shi95, Reams97, Rowbury97, Pruss97, Kikuchi98, Kikuchi98, Neely96, Popkin80, Beretskene80, Watson92]. cadBA is positively regulated by CadC [Watson92].

Citations: [Tabor83, Maurelli98, McCormick99, Day01, Park96a, Kuper05]

Locations: cytosol

Map Position: [4,354,493 <- 4,356,640] (93.85 centisomes)
Length: 2148 bp / 715 aa

Molecular Weight of Polypeptide: 81.26 kD (from nucleotide sequence)

Molecular Weight of Multimer: 81 kD (experimental) [Meng92]

pI: 6.28

Isozyme Sequence Similarity:
LdcC: YES

Unification Links: ASAP:ABE-0013526 , CGSC:943 , DIP:DIP-35646N , EchoBASE:EB0129 , EcoGene:EG10131 , EcoliWiki:b4131 , Mint:MINT-1234345 , ModBase:P0A9H3 , OU-Microarray:b4131 , PortEco:cadA , PR:PRO_000022240 , Protein Model Portal:P0A9H3 , RefSeq:NP_418555 , RegulonDB:EG10131 , SMR:P0A9H3 , String:511145.b4131 , UniProt:P0A9H3

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 , PDB:Structure:3N75 , PDB:Structure:3Q16 , 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: ?

Genetic Regulation 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 [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Snider06, Butland05]
GO:0008923 - lysine decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01, Kikuchi97a, Goldemberg80]
GO:0042802 - identical protein binding Inferred from experiment [Kanjee11a, Snider06]
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 [UniProtGOA11, UniProtGOA11a, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations pH

Essentiality data for cadA 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]

Credits:
Last-Curated ? 16-Apr-2007 by Johnson A , TIGR


Enzymatic reaction of: lysine decarboxylase

Synonyms: lysine decarboxylase, inducible, LDC, L-lysine carboxy-lyase, acid-inducible LDC

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.

Alternative Substrates for L-lysine: selenalysine , thialysine , 5-hydroxy-L-lysine [Sabo74a ]

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

Summary:
The enzyme was first studied in E. coli B [Sher54a, Sher54b, Sabo74a, Sabo74].

The cadA encoded enzyme is more active, is thermostable, and has a lower pH optimum than the other enzyme [Lemonnier98].

The Km of lysine decarboxylase is measured to be 2.0 mM [Vienozinskiene85]. Constitutive and inducible forms are observed [Goldemberg80]. The low-level activity observed under noninducing conditions is sensitive to putrescine and spermidine [Wertheimer83].

Enzyme activity assays are presented [Vienozinskiene85].

Citations: [Kamio83]

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Sabo74]

Inhibitors (Competitive): 6-aminohexanoate [Sabo74a]

Kinetic Parameters:

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

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

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


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 367
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4131 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10131; confirmed by SwissProt match.


References

Auger89: Auger EA, Redding KE, Plumb T, Childs LC, Meng SY, Bennett GN (1989). "Construction of lac fusions to the inducible arginine- and lysine decarboxylase genes of Escherichia coli K12." Mol Microbiol 3(5);609-20. PMID: 2527331

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

Beretskene80: Beretskene SIa, Bruzgulis PA, Ragavichus AB (1980). "[Conditions of the synthesis of lysine decarboxylase by Escherichia coli MRE 600]." Prikl Biokhim Mikrobiol 16(3);351-5. PMID: 7001435

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

Day01: Day WA, Fernandez RE, Maurelli AT (2001). "Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp." Infect Immun 69(12);7471-80. PMID: 11705922

Dell94: Dell CL, Neely MN, Olson ER (1994). "Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia coli cadBA operon." Mol Microbiol 14(1);7-16. PMID: 7830562

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

El10: El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA (2010). "Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity." Proc Natl Acad Sci U S A 107(52);22499-504. PMID: 21148420

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

Kamio83: Kamio Y, Terawaki Y (1983). "Purification and properties of Selenomonas ruminantium lysine decarboxylase." J Bacteriol 153(2);658-64. PMID: 6401702

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

Kuper05: Kuper C, Jung K (2005). "CadC-mediated activation of the cadBA promoter in Escherichia coli." J Mol Microbiol Biotechnol 10(1);26-39. PMID: 16491024

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

Mandic98: Mandic A (1998). "Effects of cadA gene on cell division phenotype." Med Pregl 51(1-2);21-8. PMID: 9531770

Maurelli98: Maurelli AT, Fernandez RE, Bloch CA, Rode CK, Fasano A (1998). ""Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli." Proc Natl Acad Sci U S A 95(7);3943-8. PMID: 9520472

McCormick99: McCormick BA, Fernandez MI, Siber AM, Maurelli AT (1999). "Inhibition of Shigella flexneri-induced transepithelial migration of polymorphonuclear leucocytes by cadaverine." Cell Microbiol 1(2);143-55. PMID: 11207548

Meng92: Meng SY, Bennett GN (1992). "Nucleotide sequence of the Escherichia coli cad operon: a system for neutralization of low extracellular pH." J Bacteriol 1992;174(8);2659-69. PMID: 1556085

Meng92a: Meng SY, Bennett GN (1992). "Regulation of the Escherichia coli cad operon: location of a site required for acid induction." J Bacteriol 174(8);2670-8. PMID: 1556086

Moreau07: Moreau PL (2007). "The lysine decarboxylase CadA protects Escherichia coli starved of phosphate against fermentation acids." J Bacteriol 189(6);2249-61. PMID: 17209032

Neely94: Neely MN, Dell CL, Olson ER (1994). "Roles of LysP and CadC in mediating the lysine requirement for acid induction of the Escherichia coli cad operon." J Bacteriol 176(11);3278-85. PMID: 8195083

Neely96: Neely MN, Olson ER (1996). "Kinetics of expression of the Escherichia coli cad operon as a function of pH and lysine." J Bacteriol 178(18);5522-8. PMID: 8808945

Park96a: Park YK, Bearson B, Bang SH, Bang IS, Foster JW (1996). "Internal pH crisis, lysine decarboxylase and the acid tolerance response of Salmonella typhimurium." Mol Microbiol 20(3);605-11. PMID: 8736539

Popkin80: Popkin PS, Maas WK (1980). "Escherichia coli regulatory mutation affecting lysine transport and lysine decarboxylase." J Bacteriol 141(2);485-92. PMID: 6767681

Pruss97: Pruss BM, Markovic D, Matsumura P (1997). "The Escherichia coli flagellar transcriptional activator flhD regulates cell division through induction of the acid response gene cadA." J Bacteriol 179(11);3818-21. PMID: 9171439

Reams97: Reams SG, Lee N, Mat-Jan F, Clark DP (1997). "Effect of chelating agents and respiratory inhibitors on regulation of the cadA gene in Escherichia coli." Arch Microbiol 167(4);209-16. PMID: 9075621

Rowbury97: Rowbury RJ (1997). "Regulatory components, including integration host factor, CysB and H-NS, that influence pH responses in Escherichia coli." Lett Appl Microbiol 24(5);319-28. PMID: 9172436

Sabo74: Sabo DL, Fischer EH (1974). "Chemical properties of Escherichia coli lysine decarboxylase including a segment of its pyridoxal 5'-phosphate binding site." Biochemistry 13(4);670-6. PMID: 4204273

Sabo74a: Sabo DL, Boeker EA, Byers B, Waron H, Fischer EH (1974). "Purification and physical properties of inducible Escherichia coli lysine decarboxylase." Biochemistry 1974;13(4);662-70. PMID: 4590109

Sher54a: Sher IH, Mallette MF (1954). "The adaptive nature of the formation of lysine decarboxylase in Escherichia coli B." Arch Biochem Biophys 52(2);331-9. PMID: 13208257

Sher54b: Sher IH, Mallette MF (1954). "Purification and study of L-lysine decarboxylase from Escherichia coli B." Arch Biochem Biophys 53(2);354-69. PMID: 13218704

Shi93: Shi X, Waasdorp BC, Bennett GN (1993). "Modulation of acid-induced amino acid decarboxylase gene expression by hns in Escherichia coli." J Bacteriol 175(4);1182-6. PMID: 8381784

Shi95: Shi X, Bennett GN (1995). "Effects of multicopy LeuO on the expression of the acid-inducible lysine decarboxylase gene in Escherichia coli." J Bacteriol 177(3);810-4. PMID: 7836317

Snider06: Snider J, Gutsche I, Lin M, Baby S, Cox B, Butland G, Greenblatt J, Emili A, Houry WA (2006). "Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase." J Biol Chem 281;1532-1546. PMID: 16301313

Tabor80: Tabor H, Hafner EW, Tabor CW (1980). "Construction of an Escherichia coli strain unable to synthesize putrescine, spermidine, or cadaverine: characterization of two genes controlling lysine decarboxylase." J Bacteriol 144(3);952-6. PMID: 7002915

Tabor83: Tabor CW, Tabor H, Hafner EH (1983). "Mass screening for mutants in the biosynthetic pathway for polyamines in Escherichia coli: a general method for mutants in enzymatic reactions producing CO2." Methods Enzymol 94;83-91. PMID: 6413821

Takayama94: Takayama M, Ohyama T, Igarashi K, Kobayashi H (1994). "Escherichia coli cad operon functions as a supplier of carbon dioxide." Mol Microbiol 11(5);913-8. PMID: 8022268

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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Watson92: Watson N, Dunyak DS, Rosey EL, Slonczewski JL, Olson ER (1992). "Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH." J Bacteriol 174(2);530-40. PMID: 1370290

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

Other References Related to Gene Regulation

Bi14: Bi H, Zhang C (2014). "Integration host factor is required for the induction of acid resistance in Escherichia coli." Curr Microbiol 69(2);218-24. PMID: 24816374

Fritz09: Fritz G, Koller C, Burdack K, Tetsch L, Haneburger I, Jung K, Gerland U (2009). "Induction kinetics of a conditional pH stress response system in Escherichia coli." J Mol Biol 393(2);272-86. PMID: 19703467

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

Krin10: Krin E, Danchin A, Soutourina O (2010). "Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli." BMC Microbiol 10;273. PMID: 21034467

Krin10a: Krin E, Danchin A, Soutourina O (2010). "RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli." Res Microbiol 161(5);363-371. PMID: 20435136

Laurent88: Laurent G, Calemard E, Charra B (1988). "Dialysis related amyloidosis." Kidney Int Suppl 24;S32-4. PMID: 3163049

Liu04: Liu X, De Wulf P (2004). "Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling." J Biol Chem 279(13);12588-97. PMID: 14711822

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697

Ruiz11: Ruiz J, Haneburger I, Jung K (2011). "Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli." J Bacteriol 193(10);2536-48. PMID: 21441513

Tetsch08: Tetsch L, Koller C, Haneburger I, Jung K (2008). "The membrane-integrated transcriptional activator CadC of Escherichia coli senses lysine indirectly via the interaction with the lysine permease LysP." Mol Microbiol 67(3);570-83. PMID: 18086202

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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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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