|Gene:||lpxC||Accession Numbers: EG10265 (EcoCyc), b0096, ECK0097|
Synonyms: asmB, envA
UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) catalyzes the second reaction and the first committed step in lipid A biosynthesis. LpxC hydrolyzes UDP-3-O-(3-hydroxymyristoyl)-N-acetlyglucosamine to UDP-3-O-(3-hydroxymyristoyl)glucosamine and acetate [Young95, Anderson88a]. The mechanism of action of LpxC has been studied, and a high-throughput fluorescent screen as well as a mass-spectrometry based screen have been developed to evaluate LpxC activity [Hernick05, Wang01d, Langsdorf10].
LpxC is a metalloenzyme that requires bound zinc for activity [Jackman99]. More recently, LpxC with bound iron was shown to have higher activity than zinc as the cofactor [Hernick10]. LpxC has significantly higher affinity for zinc, however, the in vivo concentrations of readily available iron are higher. The ability of LpxC to switch between metal ions in response to availability has been proposed. [Gattis10] SIte directed mutagenesis has identified zinc binding sites [Jackman01].
LpxC abundance is regulated in response to the cell's need for lipid A [Sorensen96a]. This regulation occurs via degradation by HflB, integral membrane ATP-dependent zinc metallopeptidase, and requires the presence of the carboxy-terminus of LpxC which contains a signal sequence necessary for this FtsH-dependent degradation [Ogura99, Fuhrer06]. LpxC is degraded by FtsH in a growth-rate dependent manner, where LpxC is degraded during slow growth, and stabilized when cells grow rapidly [Schakermann13].
lpxC is an essential gene [Beall87]. Mutations in lpxC lead to problems with cell division, increased permeability to antibacterial agents, leakage of periplasmic enzymes and reduced abundance of LPS [Normark69, Normark70, Young91a, Kloser96].
LpxC is a drug target for antimicrobials due to its role in lipid A synthesis [Onishi96]. Various inhibitors of LpxC have been discovered [Clements02, Jackman00, Barb08, Liang11, Liang13, Loppenberg13]. The molecular determinants of binding and specificity as well as the catalytic mechanism have been studied with respect to drug development [Hernick06]. Spontaneous mutants which were resistant to LpxC inhibitors were isolated and found to have mutations in fabZ or thrS [Zeng13a].
The crystal structure of LpxC in complex with UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine was determined [Clayton13]. The crystal structure analysis of LpxC bound to an inhibitor revealed a backbone flipping of a loop causing a conformational switch allowing for expansion of the active site and thereby accomodating LpxC inhibitors with different head groups [Lee13b].
|Map Position: [106,557 -> 107,474] (2.3 centisomes, 8°)||Length: 918 bp / 305 aa|
Molecular Weight of Polypeptide: 33.956 kD (from nucleotide sequence), 33.96 kD (experimental) [Jackman99 ]
Unification Links: ASAP:ABE-0000336 , CGSC:815 , DIP:DIP-48045N , EchoBASE:EB0261 , EcoGene:EG10265 , EcoliWiki:b0096 , Mint:MINT-1309717 , ModBase:P0A725 , OU-Microarray:b0096 , PortEco:lpxC , PR:PRO_000023122 , Protein Model Portal:P0A725 , RefSeq:NP_414638 , RegulonDB:EG10265 , SMR:P0A725 , String:511145.b0096 , UniProt:P0A725
|Biological Process:||GO:0009245 - lipid A biosynthetic process
[UniProtGOA11a, GOA06, GOA01a, Young95]
GO:0006629 - lipid metabolic process [UniProtGOA11a]
|Molecular Function:||GO:0005506 - iron ion binding
GO:0008270 - zinc ion binding [Jackman99]
GO:0008759 - UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity [GOA06, GOA01a, Jackman99]
GO:0019213 - deacetylase activity [Anderson88a]
GO:0016787 - hydrolase activity [UniProtGOA11a]
|Cellular Component:||GO:0005737 - cytoplasm
GO:0005829 - cytosol [DiazMejia09]
|MultiFun Terms:||cell structure → surface antigens (ECA, O antigen of LPS)|
|metabolism → biosynthesis of macromolecules (cellular constituents) → lipopolysaccharide → lipid A|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Enzymatic reaction of: UDP-3-O-acyl-N-acetylglucosamine deacetylase
EC Number: 184.108.40.206
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 irreversible in the direction shown.
Primary Physiological Regulators of Enzyme Activity: Zn2+
|Metal-Binding-Site||79, 238, 246, 265|
10/20/97 Gene b0096 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10265; confirmed by SwissProt match.
Anderson88a: Anderson MS, Robertson AD, Macher I, Raetz CR (1988). "Biosynthesis of lipid A in Escherichia coli: identification of UDP-3-O-[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine as a precursor of UDP-N2,O3-bis[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine." Biochemistry 1988;27(6);1908-17. PMID: 3288280
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
Clayton13: Clayton GM, Klein DJ, Rickert KW, Patel SB, Kornienko M, Zugay-Murphy J, Reid JC, Tummala S, Sharma S, Singh SB, Miesel L, Lumb KJ, Soisson SM (2013). "Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer." J Biol Chem. PMID: 24108127
Clements02: Clements JM, Coignard F, Johnson I, Chandler S, Palan S, Waller A, Wijkmans J, Hunter MG (2002). "Antibacterial activities and characterization of novel inhibitors of LpxC." Antimicrob Agents Chemother 46(6);1793-9. PMID: 12019092
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
Gattis10: Gattis SG, Hernick M, Fierke CA (2010). "Active site metal ion in UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) switches between Fe(II) and Zn(II) depending on cellular conditions." J Biol Chem 285(44);33788-96. PMID: 20709752
Hara97: Hara H, Yasuda S, Horiuchi K, Park JT (1997). "A promoter for the first nine genes of the Escherichia coli mra cluster of cell division and cell envelope biosynthesis genes, including ftsI and ftsW." J Bacteriol 179(18);5802-11. PMID: 9294438
Hernick05: Hernick M, Gennadios HA, Whittington DA, Rusche KM, Christianson DW, Fierke CA (2005). "UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism." J Biol Chem 280(17);16969-78. PMID: 15705580
Hernick06: Hernick M, Fierke CA (2006). "Catalytic mechanism and molecular recognition of E. coli UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase probed by mutagenesis." Biochemistry 45(51);15240-8. PMID: 17176046
Hernick10: Hernick M, Gattis SG, Penner-Hahn JE, Fierke CA (2010). "Activation of Escherichia coli UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase by Fe2+ yields a more efficient enzyme with altered ligand affinity." Biochemistry 49(10);2246-55. PMID: 20136146
Jackman00: Jackman JE, Fierke CA, Tumey LN, Pirrung M, Uchiyama T, Tahir SH, Hindsgaul O, Raetz CR (2000). "Antibacterial agents that target lipid A biosynthesis in gram-negative bacteria. Inhibition of diverse UDP-3-O-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs." J Biol Chem 275(15);11002-9. PMID: 10753902
Jackman01: Jackman JE, Raetz CR, Fierke CA (2001). "Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site." Biochemistry 40(2);514-23. PMID: 11148046
Jackman99: Jackman JE, Raetz CR, Fierke CA (1999). "UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase of Escherichia coli is a zinc metalloenzyme." Biochemistry 1999;38(6);1902-11. PMID: 10026271
Kloser96: Kloser AW, Laird MW, Misra R (1996). "asmB, a suppressor locus for assembly-defective OmpF mutants of Escherichia coli, is allelic to envA (lpxC)." J Bacteriol 178(17);5138-43. PMID: 8752330
Langklotz11: Langklotz S, Schakermann M, Narberhaus F (2011). "Control of lipopolysaccharide biosynthesis by FtsH-mediated proteolysis of LpxC is conserved in enterobacteria but not in all gram-negative bacteria." J Bacteriol 193(5);1090-7. PMID: 21193611
Langsdorf10: Langsdorf EF, Malikzay A, Lamarr WA, Daubaras D, Kravec C, Zhang R, Hart R, Monsma F, Black T, Ozbal CC, Miesel L, Lunn CA (2010). "Screening for antibacterial inhibitors of the UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) using a high-throughput mass spectrometry assay." J Biomol Screen 15(1);52-61. PMID: 20019290
Liang11: Liang X, Lee CJ, Chen X, Chung HS, Zeng D, Raetz CR, Li Y, Zhou P, Toone EJ (2011). "Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold." Bioorg Med Chem 19(2);852-60. PMID: 21194954
Loppenberg13: Loppenberg M, Muller H, Pulina C, Oddo A, Teese M, Jose J, Holl R (2013). "Synthesis and biological evaluation of flexible and conformationally constrained LpxC inhibitors." Org Biomol Chem 11(36);6056-70. PMID: 23917427
McClure03: McClure CP, Rusche KM, Peariso K, Jackman JE, Fierke CA, Penner-Hahn JE (2003). "EXAFS studies of the zinc sites of UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC)." J Inorg Biochem 94(1-2);78-85. PMID: 12620676
MenginLecreulx98: Mengin-Lecreulx D, Ayala J, Bouhss A, van Heijenoort J, Parquet C, Hara H (1998). "Contribution of the Pmra promoter to expression of genes in the Escherichia coli mra cluster of cell envelope biosynthesis and cell division genes." J Bacteriol 180(17);4406-12. PMID: 9721276
Normark70: Normark S (1970). "Genetics of a chain-forming mutant of Escherichia coli. Transduction and dominance of the envA gene mediating increased penetration to some antibacterial agents." Genet Res 16(1);63-78. PMID: 4922970
Ogura99: Ogura T, Inoue K, Tatsuta T, Suzaki T, Karata K, Young K, Su LH, Fierke CA, Jackman JE, Raetz CR, Coleman J, Tomoyasu T, Matsuzawa H (1999). "Balanced biosynthesis of major membrane components through regulated degradation of the committed enzyme of lipid A biosynthesis by the AAA protease FtsH (HflB) in Escherichia coli." Mol Microbiol 31(3);833-44. PMID: 10048027
Onishi96: Onishi HR, Pelak BA, Gerckens LS, Silver LL, Kahan FM, Chen MH, Patchett AA, Galloway SM, Hyland SA, Anderson MS, Raetz CR (1996). "Antibacterial agents that inhibit lipid A biosynthesis." Science 274(5289);980-2. PMID: 8875939
Schakermann13: Schakermann M, Langklotz S, Narberhaus F (2013). "FtsH-mediated coordination of lipopolysaccharide biosynthesis in Escherichia coli correlates with the growth rate and the alarmone (p)ppGpp." J Bacteriol 195(9);1912-9. PMID: 23417489
Sorensen96a: Sorensen PG, Lutkenhaus J, Young K, Eveland SS, Anderson MS, Raetz CR (1996). "Regulation of UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase in Escherichia coli. The second enzymatic step of lipid a biosynthesis." J Biol Chem 271(42);25898-905. PMID: 8824222
Wang01d: Wang W, Maniar M, Jain R, Jacobs J, Trias J, Yuan Z (2001). "A fluorescence-based homogeneous assay for measuring activity of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase." Anal Biochem 290(2);338-46. PMID: 11237337
Westphal12: Westphal K, Langklotz S, Thomanek N, Narberhaus F (2012). "A trapping approach reveals novel substrates and physiological functions of the essential protease FtsH in Escherichia coli." J Biol Chem 287(51);42962-71. PMID: 23091052
Young95: Young K, Silver LL, Bramhill D, Cameron P, Eveland SS, Raetz CR, Hyland SA, Anderson MS (1995). "The envA permeability/cell division gene of Escherichia coli encodes the second enzyme of lipid A biosynthesis. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase." J Biol Chem 270(51);30384-91. PMID: 8530464
Eraso14: Eraso JM, Markillie LM, Mitchell HD, Taylor RC, Orr G, Margolin W (2014). "The Highly Conserved MraZ Protein Is a Transcriptional Regulator in Escherichia coli." J Bacteriol 196(11);2053-66. PMID: 24659771
Gohler11: Gohler AK, Kokpinar O, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011). "More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli." BMC Syst Biol 5(1);197. PMID: 22168595
Ishino89: Ishino F, Jung HK, Ikeda M, Doi M, Wachi M, Matsuhashi M (1989). "New mutations fts-36, lts-33, and ftsW clustered in the mra region of the Escherichia coli chromosome induce thermosensitive cell growth and division." J Bacteriol 171(10);5523-30. PMID: 2676977
MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305
©2015 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493