RegulonDB RegulonDB 10.8: Gene Form
   

gnd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gnd ugd insH7 gndA anti-anti-terminator anti-terminator terminator anti-anti-terminator anti-terminator TSS_2378 TSS_2378 TSS_2377 TSS_2377 TSS_2376 TSS_2376 gndp gndp TSS_2374 TSS_2374 TSS_2373 (cluster) TSS_2373 (cluster) TSS_2372 (cluster) TSS_2372 (cluster) TSS_2371 TSS_2371 TSS_2370 TSS_2370 TSS_2369 TSS_2369 TSS_2368 TSS_2368 ugdp9 ugdp9 cldp10 cldp10

Gene      
Name: gnd    Texpresso search in the literature
Synonym(s): ECK2024, EG10411, b2029
Genome position(nucleotides): 2099862 <-- 2101268 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.18
External database links:  
ASAP:
 ABE-0006737
CGSC:
 669
ECHOBASE:
 EB0406
OU-MICROARRAY:
 b2029
PortEco:
 gnd
STRING:
 511145.b2029
COLOMBOS: gnd


Product      
Name: 6-phosphogluconate dehydrogenase, decarboxylating
Synonym(s): Gnd
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 51.481
Isoelectric point: 4.774
Motif(s):
 
Type Positions Sequence
422 -> 422 S
170 -> 170 V
186 -> 187 HN
315 -> 315 A
5 -> 174 QIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIG

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.2 - pentose pwy, oxidative branch
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016491 - oxidoreductase activity
GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0050661 - NADP binding
biological_process GO:0009051 - pentose-phosphate shunt, oxidative branch
GO:0006098 - pentose-phosphate shunt
GO:0019521 - D-gluconate metabolic process
GO:0055114 - oxidation-reduction process
GO:0046177 - D-gluconate catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Avitabile A., et al., 1973
[2] Barcak GJ., et al., 1988
[3] Barcak GJ., et al., 1988
[4] Barcak GJ., et al., 1986
[5] Bisercic M., et al., 1991
[6] Callura JM., et al., 2012
[7] Doelle HW., et al., 1978
[8] Dykhuizen D., et al., 1980
[9] Dykhuizen DE., et al., 1991
[10] Fuhrman LK., et al., 1998
[11] Hartl DL., et al., 1981
[12] Hartl DL., et al., 1994
[13] Isturiz T., et al., 1975
[14] Jiao Z., et al., 2003
[15] Kabir MM., et al., 2004
[16] Kornberg HL., et al., 1973
[17] Lecointre G., et al., 1998
[18] Matsuoka Y., et al., 2014
[19] Miller RD., et al., 1984
[20] Nasoff MS., et al., 1980
[21] Oh MK., et al., 2000
[22] Orlowski M., et al., 1975
[23] Peng L., et al., 2004
[24] Persson B., et al., 1991
[25] Peskov K., et al., 2012
[26] Peyru G., et al., 1968
[27] Sandoval JM., et al., 2015
[28] Sawyer S. 1989
[29] Sawyer SA., et al., 1987
[30] Schreyer R., et al., 1973
[31] Shimizu K. 2004
[32] Siddiquee KA., et al., 2004
[33] Sunshine MG., et al., 1971
[34] Thomson J., et al., 1979
[35] Veronese FM., et al., 1975
[36] Veronese FM., et al., 1976
[37] Wolf RE., et al., 1980
[38] Wolf RE., et al., 1974
[39] Zhang X., et al., 2011
[40] Zhang XY., et al., 2007
[41] de Silva AO., et al., 1979
External database links:  
DIP:
 DIP-9819N
ECOCYC:
 6PGLUCONDEHYDROG-MONOMER
ECOLIWIKI:
 b2029
INTERPRO:
 IPR006114
INTERPRO:
 IPR006113
INTERPRO:
 IPR036291
INTERPRO:
 IPR013328
INTERPRO:
 IPR008927
INTERPRO:
 IPR006183
INTERPRO:
 IPR006115
INTERPRO:
 IPR006184
MODBASE:
 P00350
PANTHER:
 PTHR11811
PDB:
 2ZYD
PDB:
 2ZYA
PDB:
 3FWN
PFAM:
 PF03446
PFAM:
 PF00393
PRIDE:
 P00350
PRINTS:
 PR00076
PROSITE:
 PS00461
REFSEQ:
 NP_416533
SMART:
 SM01350
SMR:
 P00350
SWISSMODEL:
 P00350
UNIPROT:
 P00350


Operon      
Name: gnd         
Operon arrangement:
Transcription unit        Promoter
gnd


Transcriptional Regulation      
Display Regulation             
Activated by: GadE
Repressed by: Fur, FNR
Growth Conditions:

[1] 

C: Escherichia coli| MOPS| acetate 4 g/L| exponential phase
E: Escherichia coli| MOPS| acetate 4 g/L; rifampicin 500 µg/mL| exponential phase

[2] 

C: Escherichia coli| MOPS| glucose 4 g/L| exponential phase
E: Escherichia coli| MOPS| glucose 4 g/L; rifampicin 500 µg/mL| exponential phase

[3] 

C: Escherichia coli| MOPS| acetate 4 g/L| exponential phase
E: Escherichia coli| MOPS| glucose 4 g/L| exponential phase


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 cldp10 2098475 reverse Similarity to the consensus
Read more > 		[ICWHO] [42]
  promoter ugdp9 2099735 reverse Similarity to the consensus
Read more > 		[ICWHO] [42]
  promoter TSS_2368 2100229 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2369 2100231 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2370 2100277 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2371 2101069 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2372 (cluster) 2101178 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [43]
  promoter TSS_2373 (cluster) 2101320 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [43]
  promoter TSS_2374 2101322 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2376 2101396 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2377 2101409 reverse nd [RS-EPT-CBR] [43]
  promoter TSS_2378 2101436 reverse nd [RS-EPT-CBR] [43]


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] Avitabile A., Bruni CB., Carlomagno-Cerillo MS., Meyers M., Vigliar G., Blasi F., 1973, Deletion mapping and orientation of the histidine operon of Escherichia coli on a transducing bacteriophage., J Bacteriol 116(2):656-62

 [2] Barcak GJ., Wolf RE., 1988, Growth-rate-dependent expression and cloning of gnd alleles from natural isolates of Escherichia coli., J Bacteriol 170(1):365-71

 [3] Barcak GJ., Wolf RE., 1988, Comparative nucleotide sequence analysis of growth-rate-regulated gnd alleles from natural isolates of Escherichia coli and from Salmonella typhimurium LT-2., J Bacteriol 170(1):372-9

 [4] Barcak GJ., Wolf RE., 1986, A method for unidirectional deletion mutagenesis with application to nucleotide sequencing and preparation of gene fusions., Gene 49(1):119-28

 [5] Bisercic M., Feutrier JY., Reeves PR., 1991, Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus., J Bacteriol 173(12):3894-900

 [6] Callura JM., Cantor CR., Collins JJ., 2012, Genetic switchboard for synthetic biology applications., Proc Natl Acad Sci U S A 109(15):5850-5

 [7] Doelle HW., Hollywood NW., 1978, Transitional steady-state investigations during aerobic-anaerobic transition of glucose utilization by Escherichia coli K-12., Eur J Biochem 83(2):479-84

 [8] Dykhuizen D., Hartl DL., 1980, Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background., Genetics 96(4):801-17

 [9] Dykhuizen DE., Green L., 1991, Recombination in Escherichia coli and the definition of biological species., J Bacteriol 173(22):7257-68

 [10] Fuhrman LK., Wanken A., Nickerson KW., Conway T., 1998, Rapid accumulation of intracellular 2-keto-3-deoxy-6-phosphogluconate in an Entner-Doudoroff aldolase mutant results in bacteriostasis., FEMS Microbiol Lett 159(2):261-6

 [11] Hartl DL., Dykhuizen DE., 1981, Potential for selection among nearly neutral allozymes of 6-phosphogluconate dehydrogenase in Escherichia coli., Proc Natl Acad Sci U S A 78(10):6344-8

 [12] Hartl DL., Moriyama EN., Sawyer SA., 1994, Selection intensity for codon bias., Genetics 138(1):227-34

 [13] Isturiz T., Wolf RE., 1975, In vitro synthesis of a constitutive enzyme of Escherichia coli, 6-phosphogluconate dehydrogenase., Proc Natl Acad Sci U S A 72(11):4381-4

 [14] Jiao Z., Baba T., Mori H., Shimizu K., 2003, Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement., FEMS Microbiol Lett 220(2):295-301

 [15] Kabir MM., Shimizu K., 2004, Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements., Appl Microbiol Biotechnol 65(1):84-96

 [16] Kornberg HL., Soutar AK., 1973, Utilization of gluconate by Escherichia coli. Induction of gluconate kinase and 6-phosphogluconate dehydratase activities., Biochem J 134(2):489-98

 [17] Lecointre G., Rachdi L., Darlu P., Denamur E., 1998, Escherichia coli molecular phylogeny using the incongruence length difference test., Mol Biol Evol 15(12):1685-95

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

 [19] Miller RD., Dykhuizen DE., Green L., Hartl DL., 1984, Specific deletion occurring in the directed evolution of 6-phosphogluconate dehydrogenase in Escherichia coli., Genetics 108(4):765-72

 [20] Nasoff MS., Wolf RE., 1980, Molecular cloning, correlation of genetic and restriction maps, and determination of the direction of transcription of gnd of Escherichia coli., J Bacteriol 143(2):731-41

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

 [22] Orlowski M., Goldman M., 1975, Effect of chlorpromazine on the respiration and hexose monophosphate dehydrogenases of gram-negative bacteria., Can J Microbiol 21(3):415-7

 [23] Peng L., Shimizu K., 2004, Effect of ppc gene knockout on the metabolism of Escherichia coli in view of gene expressions, enzyme activities and intracellular metabolite concentrations., Appl Microbiol Biotechnol

 [24] Persson B., Jeffery J., Jornvall H., 1991, Different segment similarities in long-chain dehydrogenases., Biochem Biophys Res Commun 177(1):218-23

 [25] Peskov K., Mogilevskaya E., Demin O., 2012, Kinetic modelling of central carbon metabolism in Escherichia coli., FEBS J 279(18):3374-85

 [26] Peyru G., Fraenkel DG., 1968, Genetic mapping of loci for glucose-6-phosphate dehydrogenase, gluconate-6-phosphate dehydrogenase, and gluconate-6-phosphate dehydrase in Escherichia coli., J Bacteriol 95(4):1272-8

 [27] Sandoval JM., Arenas FA., Garcia JA., Diaz-Vasquez WA., Valdivia-Gonzalez M., Sabotier M., Vasquez CC., 2015, Escherichia coli 6-phosphogluconate dehydrogenase aids in tellurite resistance by reducing the toxicant in a NADPH-dependent manner., Microbiol Res 177:22-7

 [28] Sawyer S., 1989, Statistical tests for detecting gene conversion., Mol Biol Evol 6(5):526-38

 [29] Sawyer SA., Dykhuizen DE., Hartl DL., 1987, Confidence interval for the number of selectively neutral amino acid polymorphisms., Proc Natl Acad Sci U S A 84(17):6225-8

 [30] Schreyer R., Bock A., 1973, Phenotypic suppression of a fructose-1,6-diphosphate aldolase mutation in Escherichia coli., J Bacteriol 115(1):268-76

 [31] Shimizu K., 2004, Metabolic flux analysis based on 13C-labeling experiments and integration of the information with gene and protein expression patterns., Adv Biochem Eng Biotechnol 91:1-49

 [32] Siddiquee KA., Arauzo-Bravo MJ., Shimizu K., 2004, Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli., FEMS Microbiol Lett 235(1):25-33

 [33] Sunshine MG., Kelly B., 1971, Extent of host deletions associated with bacteriophage P2-mediated eduction., J Bacteriol 108(2):695-704

 [34] Thomson J., Gerstenberger PD., Goldberg DE., Gociar E., Orozco de Silva A., Fraenkel DG., 1979, ColE1 hybrid plasmids for Escherichia coli genes of glycolysis and the hexose monophosphate shunt., J Bacteriol 137(1):502-6

 [35] Veronese FM., Boccu E., Fontana A., 1975, Denaturation of thermophilic and mesophilic 6-phosphogluconate dehydrogenase by 8M urea., Int J Pept Protein Res 7(4):341-3

 [36] Veronese FM., Grandi C., Boccu E., Fontana A., 1976, Comparative conformational properties of thermophilic and mesophilic 6-phosphogluconate dehydrogenase., Experientia Suppl 26:147-55

 [37] Wolf RE., Cool JA., 1980, Mapping of insertion mutations in gnd of Escherichia coli with deletions defining the ends of the gene., J Bacteriol 141(3):1222-9

 [38] Wolf RE., Fraenkel DG., 1974, Isolation of specialized transducing bacteriophages for gluconate 6-phosphate dehydrogenase (gnd) of Escherichia coli., J Bacteriol 117(2):468-76

 [39] Zhang X., Zhang Y., Li Z., Xia Y., Ye Q., 2011, Continuous culture and proteomic analysis of Escherichia coli DH5α and its acetate-tolerant mutant DA19 under conditions of nitrogen source limitation., Bioprocess Biosyst Eng 34(2):179-87

 [40] Zhang XY., Zhang YJ., Li ZM., Xia YL., Ye Q., 2007, [Effects of adenine on the growth and metabolism of Escherichia coli DH5alpha and its acetate-tolerant mutant DA19]., Wei Sheng Wu Xue Bao 47(3):430-4

 [41] de Silva AO., Fraenkel DG., 1979, The 6-phosphogluconate dehydrogenase reaction in Escherichia coli., J Biol Chem 254(20):10237-42

 [42] 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

 [43] 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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