RegulonDB RegulonDB 10.10: Gene Form
   

ppc gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ppc eptC argE Cra terminator TSS_4683 TSS_4683 TSS_4682 TSS_4682 TSS_4681 TSS_4681 TSS_4680 TSS_4680 ppcp ppcp TSS_4679 (cluster) TSS_4679 (cluster) TSS_4678 TSS_4678 TSS_4677 TSS_4677 TSS_4676 (cluster) TSS_4676 (cluster) TSS_4675 TSS_4675 TSS_4674 TSS_4674 TSS_4673 TSS_4673 TSS_4672 TSS_4672 TSS_4671 TSS_4671 TSS_4670 TSS_4670 TSS_4669 TSS_4669 TSS_4668 TSS_4668 TSS_4667 TSS_4667 TSS_4666 TSS_4666 TSS_4665 TSS_4665 TSS_4664 (cluster) TSS_4664 (cluster) TSS_4663 (cluster) TSS_4663 (cluster) TSS_4662 TSS_4662 TSS_4661 TSS_4661 TSS_4660 TSS_4660 TSS_4659 TSS_4659 TSS_4658 TSS_4658 TSS_4657 TSS_4657 TSS_4656 TSS_4656 TSS_4655 (cluster) TSS_4655 (cluster) TSS_4654 TSS_4654 yijPp9 yijPp9

Gene      
Name: ppc    Texpresso search in the literature
Synonym(s): ECK3947, EG10756, asp, b3956, glu
Genome position(nucleotides): 4150447 <-- 4153098 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.66


Product      
Name: phosphoenolpyruvate carboxylase
Synonym(s): Asp, Glu, PEPC, Ppc
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 99.062
Isoelectric point: 5.397
Motif(s):
 
Type Positions Sequence
129 -> 883 LSLELVLTAHPTEITRRTLIHKMVEVNACLKQLDNKDIADYEHNQLMRRLRQLIAQSWHTDEIRKLRPSPVDEAKWGFAVVENSLWQGVPNYLRELNEQLEENLGYKLPVEFVPVRFTSWMGGDRDGNPNVTADITRHVLLLSRWKATDLFLKDIQVLVSELSMVEATPELLALVGEEGAAEPYRYLMKNLRSRLMATQAWLEARLKGEELPKPEGLLTQNEELWEPLYACYQSLQACGMGIIANGDLLDTLRRVKCFGVPLVRIDIRQESTRHTEALGELTRYLGIGDYESWSEADKQAFLIRELNSKRPLLPRNWQPSAETREVLDTCQVIAEAPQGSIAAYVISMAKTPSDVLAVHLLLKEAGIGFAMPVAPLFETLDDLNNANDVMTQLLNIDWYRGLIQGKQMVMIGYSDSAKDAGVMAASWAQYQAQDALIKTCEKAGIELTLFHGRGGSIGRGGAPAHAALLSQPPGSLKGGLRVTEQGEMIRFKYGLPEITVSSLSLYTGAILEANLLPPPEPKESWRRIMDELSVISCDVYRGYVRENKDFVPYFRSATPEQELGKLPLGSRPAKRRPTGGVESLRAIPWIFAWTQNRLMLPAWLGAGTALQKVVEDGKQSELEAMCRDWPFFSTRLGMLEMVFAKADLWLAEYYDQRLVDKALWPLGKELRNLQEEDIKVVLAIANDSHLMADLPWIAESIQLRNIYTDPLNVLQAELLHRSRQAEKEGQEPDPRVEQALMVTIAGIAAGMRNTG
587 -> 587 R
188 -> 188 T
313 -> 313 R
620 -> 620 K

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.4 - TCA cycle
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.5 - fermentation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016829 - lyase activity
GO:0008964 - phosphoenolpyruvate carboxylase activity
GO:0000287 - magnesium ion binding
GO:0042802 - identical protein binding
biological_process GO:0008152 - metabolic process
GO:0006094 - gluconeogenesis
GO:0006099 - tricarboxylic acid cycle
GO:0015977 - carbon fixation
GO:0051289 - protein homotetramerization
GO:0006107 - oxaloacetate metabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Canovas JL., et al., 1965
[2] Chao YP., et al., 2003
[3] Chao YP., et al., 1994
[4] Coomes MW., et al., 1985
[5] Cunin R., et al., 1971
[6] De Maeseneire SL., et al., 2006
[7] De Mey M., et al., 2007
[8] De Mey M., et al., 2010
[9] De Mey M., et al., 2010
[10] Emmerling M., et al., 2002
[11] Fong SS., et al., 2006
[12] Fong SS., et al., 2004
[13] Fujita N., et al., 1984
[14] Gokarn RR., et al., 2000
[15] Ishijima S., et al., 1986
[16] Ishijima S., et al., 1985
[17] Ishijima S., et al., 1987
[18] Izui K., et al., 1981
[19] Kabir MM., et al., 2003
[20] Kameshita I., et al., 1979
[21] Kameshita I., et al., 1979
[22] Kameshita I., et al., 1978
[23] Krylov AA., et al., 2020
[24] Kwon YD., et al., 2007
[25] Kwon YD., et al., 2008
[26] Lee B., et al., 1999
[27] Liao JC., et al., 1994
[28] Lin H., et al., 2004
[29] Matsuoka Y., et al., 2014
[30] Matsuoka Y., et al., 2014
[31] Mazaitis AJ., et al., 1976
[32] Moran MC., et al., 1979
[33] Naide A., et al., 1979
[34] Noronha SB., et al., 2000
[35] Oh MK., et al., 2000
[36] Oh MK., et al., 2000
[37] Phue JN., et al., 2005
[38] Press R., et al., 1971
[39] Rubenstein P., et al., 1980
[40] Saa P., et al., 2015
[41] Sabe H., et al., 1984
[42] Schultz A., et al., 2015
[43] Shen T., et al., 2013
[44] Sigala JC., et al., 2019
[45] Soellner S., et al., 2013
[46] Tan Z., et al., 2013
[47] Terada K., et al., 1995
[48] Tokuyama K., et al., 2019
[49] Vandedrinck S., et al., 2001
[50] Wang D., et al., 2013
[51] Yang C., et al., 2003
[52] Zhao J., et al., 2004
External database links:  
DIP:
 DIP-10538N
ECOCYC:
 PEPCARBOX-MONOMER
ECOLIWIKI:
 b3956
INTERPRO:
 IPR033129
INTERPRO:
 IPR022805
INTERPRO:
 IPR015813
INTERPRO:
 IPR018129
INTERPRO:
 IPR021135
MODBASE:
 P00864
PANTHER:
 PTHR30523
PDB:
 1QB4
PDB:
 1JQN
PDB:
 1FIY
PFAM:
 PF00311
PRIDE:
 P00864
PRINTS:
 PR00150
PRODB:
 PRO_000023576
PROSITE:
 PS00393
PROSITE:
 PS00781
REFSEQ:
 NP_418391
SMR:
 P00864
UNIPROT:
 P00864


Operon      
Name: ppc         
Operon arrangement:
Transcription unit        Promoter
ppc


Transcriptional Regulation      
Display Regulation             
Repressed by: Cra


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter yijPp9 4150311 reverse nd [ICWHO] [53]
  promoter TSS_4654 4151068 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4655 (cluster) 4151679 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4656 4151684 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4657 4151686 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4658 4151694 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4659 4151698 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4660 4151717 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4661 4151894 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4662 4151903 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4663 (cluster) 4151918 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4664 (cluster) 4151922 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4665 4152046 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4666 4152049 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4667 4152053 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4668 4152060 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4669 4152085 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4670 4152149 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4671 4152153 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4672 4152158 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4673 4152164 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4674 4152443 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4675 4152528 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4676 (cluster) 4152676 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4677 4152914 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4678 4153121 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4679 (cluster) 4153188 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4680 4153572 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4681 4153575 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4682 4153694 reverse nd [RS-EPT-CBR] [54]
  promoter TSS_4683 4153697 reverse nd [RS-EPT-CBR] [54]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Canovas JL., Kornberg HL., 1965, Fine control of phosphopyruvate carboxylase activity in Escherichia coli., Biochim Biophys Acta 96:169-72

 [2] Chao YP., Chiang CJ., Wang YL., Wang ZW., 2003, Applicability of new expression vectors for both engineering uses and biological studies., Biotechnol Prog 19(3):1076-80

 [3] Chao YP., Liao JC., 1994, Metabolic responses to substrate futile cycling in Escherichia coli., J Biol Chem 269(7):5122-6

 [4] Coomes MW., Mitchell BK., Beezley A., Smith TE., 1985, Properties of an Escherichia coli mutant deficient in phosphoenolpyruvate carboxylase catalytic activity., J Bacteriol 164(2):646-52

 [5] Cunin R., Glansdorff N., 1971, Messenger RNA from arginine and phosphoenolpyruvate carboxylase genes in arg R+ and arg R(-) strains of E. coli K-12., FEBS Lett 18(1):135-137

 [6] De Maeseneire SL., De Mey M., Vandedrinck S., Vandamme EJ., 2006, Metabolic characterisation of E. coli citrate synthase and phosphoenolpyruvate carboxylase mutants in aerobic cultures., Biotechnol Lett 28(23):1945-53

 [7] De Mey M., Lequeux GJ., Beauprez JJ., Maertens J., Van Horen E., Soetaert WK., Vanrolleghem PA., Vandamme EJ., 2007, Comparison of different strategies to reduce acetate formation in Escherichia coli., Biotechnol Prog 23(5):1053-63

 [8] De Mey M., Lequeux GJ., Beauprez JJ., Maertens J., Waegeman HJ., Van Bogaert IN., Foulquie-Moreno MR., Charlier D., Soetaert WK., Vanrolleghem PA., Vandamme EJ., 2010, Transient metabolic modeling of Escherichia coli MG1655 and MG1655 DeltaackA-pta, DeltapoxB Deltapppc ppc-p37 for recombinant beta-galactosidase production., J Ind Microbiol Biotechnol 37(8):793-803

 [9] De Mey M., Maertens J., Boogmans S., Soetaert WK., Vandamme EJ., Cunin R., Foulquie-Moreno MR., 2010, Promoter knock-in: a novel rational method for the fine tuning of genes., BMC Biotechnol 10:26

 [10] Emmerling M., Dauner M., Ponti A., Fiaux J., Hochuli M., Szyperski T., Wuthrich K., Bailey JE., Sauer U., 2002, Metabolic flux responses to pyruvate kinase knockout in Escherichia coli., J Bacteriol 184(1):152-64

 [11] Fong SS., Nanchen A., Palsson BO., Sauer U., 2006, Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes., J Biol Chem 281(12):8024-33

 [12] Fong SS., Palsson BO., 2004, Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes., Nat Genet 36(10):1056-8

 [13] Fujita N., Miwa T., Ishijima S., Izui K., Katsuki H., 1984, The primary structure of phosphoenolpyruvate carboxylase of Escherichia coli. Nucleotide sequence of the ppc gene and deduced amino acid sequence., J Biochem 95(4):909-16

 [14] Gokarn RR., Eiteman MA., Altman E., 2000, Metabolic analysis of Escherichia coli in the presence and absence of the carboxylating enzymes phosphoenolpyruvate carboxylase and pyruvate carboxylase., Appl Environ Microbiol 66(5):1844-50

 [15] Ishijima S., Izui K., Katsuki H., 1986, Phosphoenolpyruvate carboxylase of Escherichia coli K-12. N- and C-terminal sequences and tentative assignment of the catalytically essential cysteine residue., J Biochem 99(5):1299-310

 [16] Ishijima S., Katagiri F., Kodaki T., Izui K., Katsuki H., Nishikawa K., Nakashima H., Ooi T., 1985, Comparison of amino acid sequences between phosphoenolpyruvate carboxylases from Escherichia coli (allosteric) and Anacystis nidulans (non-allosteric): identification of conserved and variable regions., Biochem Biophys Res Commun 133(2):436-41

 [17] Ishijima S., Taguchi M., Hirai K., Izui K., Namba Y., Hanaoka M., Katsuki H., 1987, Preparation and characterization of monoclonal antibodies against phosphoenolpyruvate carboxylase of Escherichia coli., J Biochem 102(5):1231-40

 [18] Izui K., Taguchi M., Morikawa M., Katsuki H., 1981, Regulation of Escherichia coli phosphoenolpyruvate carboxylase by multiple effectors in vivo. II. Kinetic studies with a reaction system containing physiological concentrations of ligands., J Biochem 90(5):1321-31

 [19] Kabir MM., Shimizu K., 2003, Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR., J Biotechnol 105(1-2):11-31

 [20] Kameshita I., Izui K., Katsuki H., 1979, Phosphoenolpyruvate carboxylase of Escherichia coli. Effect of proteolytic modification on the catalytic and regulatory propties., J Biochem 86(1):1-10

 [21] Kameshita I., Tokushige M., Izui K., Katsuki H., 1979, Phosphoenolpyruvate carboxylase of Escherichia coli. Affinity labeling with bromopyruvate., J Biochem 86(5):1251-7

 [22] Kameshita I., Tokushige M., Katsuki H., 1978, Phosphoenolpyruvate carboxylase of Escherichia coli. Essential arginyl residues for catalytic and regulatory functions., J Biochem 84(4):795-803

 [23] Krylov AA., Shapovalova VV., Miticheva EA., Shupletsov MS., Mashko SV., 2020, Universal Actuator for Efficient Silencing of Escherichia coli Genes Based on Convergent Transcription Resistant to Rho-Dependent Termination., ACS Synth Biol 9(7):1650-1664

 [24] Kwon YD., Kwon OH., Lee HS., Kim P., 2007, The effect of NADP-dependent malic enzyme expression and anaerobic C4 metabolism in Escherichia coli compared with other anaplerotic enzymes., J Appl Microbiol 103(6):2340-5

 [25] Kwon YD., Lee SY., Kim P., 2008, A physiology study of Escherichia coli overexpressing phosphoenolpyruvate carboxykinase., Biosci Biotechnol Biochem 72(4):1138-41

 [26] Lee B., Yen J., Yang L., Liao JC., 1999, Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic., Biotechnol Bioeng 62(6):722-9

 [27] Liao JC., Chao YP., Patnaik R., 1994, Alteration of the biochemical valves in the central metabolism of Escherichia coli., Ann N Y Acad Sci 745:21-34

 [28] Lin H., Vadali RV., Bennett GN., San KY., 2004, Increasing the acetyl-CoA pool in the presence of overexpressed phosphoenolpyruvate carboxylase or pyruvate carboxylase enhances succinate production in Escherichia coli., Biotechnol Prog 20(5):1599-604

 [29] Matsuoka Y., Shimizu K., 2014, Metabolic flux analysis for Escherichia coli by flux balance analysis., Methods Mol Biol 1191:237-60

 [30] Matsuoka Y., Shimizu K., 2014, 13C-metabolic flux analysis for Escherichia coli., Methods Mol Biol 1191:261-89

 [31] Mazaitis AJ., Palchaudhuri S., Glansdorff N., Maas WK., 1976, Isolation and characterization of lambdadargECBH transducing phages and heteroduplex analysis of the argECBH cluster., Mol Gen Genet 143(2):185-96

 [32] Moran MC., Mazaitis AJ., Vogel RH., Vogel HJ., 1979, Clustered arg genes on a BamHI segment of the Escherichia coli chromosome., Gene 8(1):25-34

 [33] Naide A., Izui K., Yoshinaga T., Katsuki H., 1979, Phosphoenolpyruvate carboxylase of Escherichia coli. The role of lysyl residues in the catalytic and regulatory functions., J Biochem 85(2):423-32

 [34] Noronha SB., Yeh HJ., Spande TF., Shiloach J., 2000, Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using (13)C-NMR/MS., Biotechnol Bioeng 68(3):316-27

 [35] Oh MK., Liao JC., 2000, Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli., Biotechnol Prog 16(2):278-86

 [36] Oh MK., Liao JC., 2000, DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli., Metab Eng 2(3):201-9

 [37] Phue JN., Noronha SB., Hattacharyya R., Wolfe AJ., Shiloach J., 2005, Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses., Biotechnol Bioeng 90(7):805-20

 [38] Press R., Glansdorff N., Miner P., De Vries J., Kadner R., Maas WK., 1971, Isolation of transducing particles of phi-80 bacteriophage that carry different regions of the Escherichia coli genome., Proc Natl Acad Sci U S A 68(4):795-8

 [39] Rubenstein P., Dryer R., 1980, S-acetonyl-CoA. A nonreactive analog of acetyl-CoA., J Biol Chem 255(16):7858-62

 [40] Saa P., Nielsen LK., 2015, A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions., PLoS Comput Biol 11(4):e1004195

 [41] Sabe H., Miwa T., Kodaki T., Izui K., Hiraga S., Katsuki H., 1984, Molecular cloning of the phosphoenolpyruvate carboxylase gene, ppc, of Escherichia coli., Gene 31(1-3):279-83

 [42] Schultz A., Qutub AA., 2015, Predicting internal cell fluxes at sub-optimal growth., BMC Syst Biol 9:18

 [43] Shen T., Rui B., Zhou H., Zhang X., Yi Y., Wen H., Zheng H., Wu J., Shi Y., 2013, Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress., Mol Biosyst 9(1):121-32

 [44] Sigala JC., Quiroz L., Arteaga E., Olivares R., Lara AR., Martinez A., 2019, Physiological and transcriptional comparison of acetate catabolism between Acinetobacter schindleri ACE and Escherichia coli JM101., FEMS Microbiol Lett 366(12)

 [45] Soellner S., Rahnert M., Siemann-Herzberg M., Takors R., Altenbuchner J., 2013, Evolution of pyruvate kinase-deficient Escherichia coli mutants enables glycerol-based cell growth and succinate production., J Appl Microbiol 115(6):1368-78

 [46] Tan Z., Zhu X., Chen J., Li Q., Zhang X., 2013, Activating phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase in combination for improvement of succinate production., Appl Environ Microbiol 79(16):4838-44

 [47] Terada K., Fujita N., Katsuki H., Izui K., 1995, Construction of a plasmid for high level expression of Escherichia coli phosphoenolpyruvate carboxylase., Biosci Biotechnol Biochem 59(4):735-7

 [48] Tokuyama K., Toya Y., Shimizu H., 2019, Prediction of Rate-Limiting Reactions for Growth-Associated Production Using a Constraint-Based Approach., Biotechnol J 14(9):e1800431

 [49] Vandedrinck S., Deschamps G., Sablon E., Vandamme EJ., 2001, Construction and characterization of a PPC (phosphoenolpyruvate carboxylase) knockout mutant of Escherichia coli., Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet 66(4):345-9

 [50] Wang D., Wang H., Wang J., Wang N., Zhang J., Xing J., 2013, [Effects of furfural and 5-hydroxymethylfurfural on succinic acid production by Escherichia coli]., Sheng Wu Gong Cheng Xue Bao 29(10):1463-72

 [51] Yang C., Hua Q., Baba T., Mori H., Shimizu K., 2003, Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout., Biotechnol Bioeng 84(2):129-44

 [52] Zhao J., Baba T., Mori H., Shimizu K., 2004, Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities., Appl Microbiol Biotechnol 64(1):91-8

 [53] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [54] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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