RegulonDB RegulonDB 10.10: Gene Form
   

glpK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

glpK glpX glpF GlpR GlpR anti-anti-terminator anti-terminator glpXp2 glpXp2 TSS_4623 TSS_4623 TSS_4622 TSS_4622

Gene      
Name: glpK    Texpresso search in the literature
Synonym(s): ECK3918, EG10398, b3926
Genome position(nucleotides): 4115714 <-- 4117222 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.08
External database links:  
ASAP:
 ABE-0012825
CGSC:
 691
ECHOBASE:
 EB0393
ECOLIHUB:
 glpK
MIM:
 600149
OU-MICROARRAY:
 b3926
STRING:
 511145.b3926
COLOMBOS: glpK


Shine dalgarno      
Sequence: atatgactacGGGACAattaaaCAT


Product      
Name: glycerol kinase
Synonym(s): GlpK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 56.231
Isoelectric point: 5.181
Motif(s):
 
Type Positions Sequence
475 -> 475 I
84 -> 85 RE
246 -> 247 DQ
305 -> 305 G
66 -> 66 A

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.6 - misc. glycerol metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0016301 - kinase activity
GO:0016773 - phosphotransferase activity, alcohol group as acceptor
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008270 - zinc ion binding
GO:0004370 - glycerol kinase activity
GO:0042802 - identical protein binding
biological_process GO:0008152 - metabolic process
GO:0005975 - carbohydrate metabolic process
GO:0006071 - glycerol metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0016310 - phosphorylation
GO:0006072 - glycerol-3-phosphate metabolic process
GO:0019563 - glycerol catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Benov L., et al., 2001
[2] Berman-Kurtz M., et al., 1971
[3] Bethell RC., et al., 1988
[4] Bettenbrock K., et al., 2006
[5] Blattler WA., et al., 1979
[6] Bock A., et al., 1966
[7] Chagneau C., et al., 2001
[8] Conrad CA., et al., 1984
[9] Cozzarelli NR., et al., 1965
[10] Cozzarelli NR., et al., 1966
[11] Durnin G., et al., 2009
[12] Feese M., et al., 1994
[13] Freedberg WB., et al., 1971
[14] Gadkar KG., et al., 2005
[15] Girard A., et al., 1991
[16] Hayashi S., et al., 1965
[17] Jin RZ., et al., 1984
[18] Kee Y., et al., 1988
[19] Kinnersley MA., et al., 2009
[20] Koyama Y., et al., 1990
[21] Krymkiewicz N., et al., 1971
[22] Lupski JR., et al., 1990
[23] Luque I., et al., 2000
[24] Muramatsu S., et al., 1989
[25] Pettigrew DW. 2009
[26] Pliura DH., et al., 1980
[27] Raj VS., et al., 2001
[28] Richey DP., et al., 1972
[29] Schlick T. 2003
[30] Schneider PB. 1977
[31] Sundararajan TA. 1963
[32] Thorner JW. 1975
[33] Vimala A., et al., 2016
External database links:  
DIP:
 DIP-36011N
ECOCYC:
 GLYCEROL-KIN-MONOMER
ECOLIWIKI:
 b3926
INTERPRO:
 IPR000577
INTERPRO:
 IPR005999
INTERPRO:
 IPR018483
INTERPRO:
 IPR018484
INTERPRO:
 IPR018485
INTERPRO:
 IPR043129
PDB:
 3EZW
PDB:
 1GLL
PDB:
 1GLJ
PDB:
 1GLF
PDB:
 1GLE
PDB:
 1GLD
PDB:
 1GLC
PDB:
 1GLB
PDB:
 1BO5
PDB:
 1BOT
PDB:
 1BU6
PDB:
 1BWF
PDB:
 1GLA
PFAM:
 PF02782
PFAM:
 PF00370
PRIDE:
 P0A6F3
PROSITE:
 PS00933
PROSITE:
 PS00445
REFSEQ:
 NP_418361
SMR:
 P0A6F3
UNIPROT:
 P0A6F3


Operon      
Name: glpFKX         
Operon arrangement:
Transcription unit        Promoter
glpFKX


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: GlpR


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 TSS_4622 4115212 forward nd [RS-EPT-CBR] [34]
  promoter TSS_4623 4115603 reverse nd [RS-EPT-CBR] [34]
  promoter glpXp2 4115606 reverse nd [ICWHO] [35]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Benov L., Al-Ibraheem J., 2001, Glycerol metabolism in superoxide dismutase-deficient Escherichia coli., Free Radic Res 35(6):867-72

 [2] Berman-Kurtz M., Lin EC., Richey DP., 1971, Promoter-like mutant with increased expression of the glycerol kinase operon of Escherichia coli., J Bacteriol 106(3):724-31

 [3] Bethell RC., Lowe G., 1988, The stereochemical course of D-glyceraldehyde-induced ATPase activity of glycerokinase from Escherichia coli., Eur J Biochem 174(2):387-9

 [4] Bettenbrock K., Fischer S., Kremling A., Jahreis K., Sauter T., Gilles ED., 2006, A quantitative approach to catabolite repression in Escherichia coli., J Biol Chem 281(5):2578-84

 [5] Blattler WA., Knowles JR., 1979, Stereochemical course of phosphokinases. The use of adenosine [gamma-(S)-16O,17O,18O]triphosphate and the mechanistic consequences for the reactions catalyzed by glycerol kinase, hexokinase, pyruvate kinase, and acetate kinase., Biochemistry 18(18):3927-33

 [6] Bock A., Neidhardt FC., 1966, Properties of a Mutant of Escherichia coli with a Temperature-sensitive Fructose-1,6-Diphosphate Aldolase., J Bacteriol 92(2):470-6

 [7] Chagneau C., Heyde M., Alonso S., Portalier R., Laloi P., 2001, External-pH-dependent expression of the maltose regulon and ompF gene in Escherichia coli is affected by the level of glycerol kinase, encoded by glpK., J Bacteriol 183(19):5675-83

 [8] Conrad CA., Stearns GW., Prater WE., Rheiner JA., Johnson JR., 1984, Characterization of a glpK transducing phage., Mol Gen Genet 193(2):376-8

 [9] Cozzarelli NR., Koch JP., Hayashi S., Lin EC., 1965, Growth stasis by accumulated L-alpha-glycerophosphate in Escherichia coli., J Bacteriol 90(5):1325-9

 [10] Cozzarelli NR., Lin EC., 1966, Chromosomal location of the structural gene for glycerol kinase in Escherichia coli., J Bacteriol 91(5):1763-6

 [11] Durnin G., Clomburg J., Yeates Z., Alvarez PJ., Zygourakis K., Campbell P., Gonzalez R., 2009, Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli., Biotechnol Bioeng 103(1):148-61

 [12] Feese M., Pettigrew DW., Meadow ND., Roseman S., Remington SJ., 1994, Cation-promoted association of a regulatory and target protein is controlled by protein phosphorylation., Proc Natl Acad Sci U S A 91(9):3544-8

 [13] Freedberg WB., Kistler WS., Lin EC., 1971, Lethal synthesis of methylglyoxal by Escherichia coli during unregulated glycerol metabolism., J Bacteriol 108(1):137-44

 [14] Gadkar KG., Doyle Iii FJ., Edwards JS., Mahadevan R., 2005, Estimating optimal profiles of genetic alterations using constraint-based models., Biotechnol Bioeng 89(2):243-51

 [15] Girard A., Merchie B., Maisterrena B., 1991, Compartmentalized system with membrane-bound glycerol kinase. Activity and product distribution versus asymmetrical substrate supply., Biochem J 274 ( Pt 3):819-24

 [16] Hayashi S., Lin EC., 1965, Capture of glycerol by cells of Escherichia coli., Biochim Biophys Acta 94:479-87

 [17] Jin RZ., Lin EC., 1984, An inducible phosphoenolpyruvate: dihydroxyacetone phosphotransferase system in Escherichia coli., J Gen Microbiol 130(1):83-8

 [18] Kee Y., Lee YS., Chung CH., Waxman L., Goldberg AL., 1988, Improved methods for purification and assay of glycerol kinase from Escherichia coli., J Chromatogr 428(2):345-51

 [19] Kinnersley MA., Holben WE., Rosenzweig F., 2009, E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli., PLoS Genet 5(11):e1000713

 [20] Koyama Y., Nakano E., 1990, Cloning of the glpK gene of Escherichia coli K-12 and its overexpression using a 'sleeper' bacteriophage vector., Agric Biol Chem 54(5):1315-6

 [21] Krymkiewicz N., Dieguez E., Rekarte UD., Zwaig N., 1971, Properties and mode of action of a bactericidal compound (=methylglyoxal) produced by a mutant of Escherichia coli., J Bacteriol 108(3):1338-47

 [22] Lupski JR., Zhang YH., Rieger M., Minter M., Hsu B., Ooi BG., Koeuth T., McCabe ER., 1990, Mutational analysis of the Escherichia coli glpFK region with Tn5 mutagenesis and the polymerase chain reaction., J Bacteriol 172(10):6129-34

 [23] Luque I., Freire E., 2000, Structural stability of binding sites: consequences for binding affinity and allosteric effects., Proteins Suppl 4:63-71

 [24] Muramatsu S., Mizuno T., 1989, Nucleotide sequence of the region encompassing the glpKF operon and its upstream region containing a bent DNA sequence of Escherichia coli., Nucleic Acids Res 17(11):4378

 [25] Pettigrew DW., 2009, Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase., Arch Biochem Biophys 492(1-2):29-39

 [26] Pliura DH., Schomburg D., Richard JP., Frey PA., Knowles JR., 1980, Stereochemical course of a phosphokinase using a chiral [18O]phosphorothioate. Comparison with the transfer of a chiral [16O,17O,18O]phosphoryl group., Biochemistry 19(2):325-9

 [27] Raj VS., Tomitori H., Yoshida M., Apirakaramwong A., Kashiwagi K., Takio K., Ishihama A., Igarashi K., 2001, Properties of a revertant of Escherichia coli viable in the presence of spermidine accumulation: increase in L-glycerol 3-phosphate., J Bacteriol 183(15):4493-8

 [28] Richey DP., Lin EC., 1972, Importance of facilitated diffusion for effective utilization of glycerol by Escherichia coli., J Bacteriol 112(2):784-90

 [29] Schlick T., 2003, Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms., Biophys J 85(1):1-4

 [30] Schneider PB., 1977, A sensitive radioenzymatic assay for glycerol and acylglycerols., J Lipid Res 18(3):396-9

 [31] Sundararajan TA., 1963, Interference with glycerokinase induction in mutants of E. coli accumulating gal-1-P., Proc Natl Acad Sci U S A 50:463-9

 [32] Thorner JW., 1975, Glycerol kinase., Methods Enzymol 42:148-56

 [33] Vimala A., Harinarayanan R., 2016, Transketolase activity modulates glycerol-3-phosphate levels in Escherichia coli., Mol Microbiol 100(2):263-77

 [34] 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.

 [35] 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

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