RegulonDB RegulonDB 10.10: Gene Form
   

glpF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

glpK glpF zapB GlpR CRP GlpR GlpR CRP GlpR GlpR GlpR TSS_4630 (cluster) TSS_4630 (cluster) TSS_4629 TSS_4629 TSS_4628 (cluster) TSS_4628 (cluster) TSS_4627 TSS_4627 TSS_4626 TSS_4626 TSS_4625 (cluster) TSS_4625 (cluster) TSS_4624 TSS_4624 zapBp1 zapBp1 glpFp glpFp

Gene      
Name: glpF    Texpresso search in the literature
Synonym(s): ECK3919, EG10396, b3927
Genome position(nucleotides): 4117245 <-- 4118090 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.95
External database links:  
ASAP:
 ABE-0012828
CGSC:
 692
ECHOBASE:
 EB0391
ECOLIHUB:
 glpF
OU-MICROARRAY:
 b3927
STRING:
 511145.b3927
COLOMBOS: glpF


Shine dalgarno      
Sequence: attaactcttCAGGATccgatTAT


Product      
Name: glycerol facilitator
Synonym(s): GlpF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 29.78
Isoelectric point: 6.649
Motif(s):
 
Type Positions Sequence
160 -> 160 M
144 -> 169 NFVQAFAVEMVITAILMGLILALTDD
168 -> 168 D
232 -> 254 YFLVPLFGPIVGAIVGAFAYRKL
2 -> 251 SQTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAY

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.4 - fatty acids and phosphatidic acid
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.6 - misc. glycerol metabolism
  4 - transport --> 4.1 - Channel-type Transporters --> 4.1.A - alpha-type channels
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0046872 - metal ion binding
GO:0015267 - channel activity
GO:0015168 - glycerol transmembrane transporter activity
GO:0005372 - water transmembrane transporter activity
GO:0015254 - glycerol channel activity
biological_process GO:0015793 - glycerol transport
GO:0006833 - water transport
GO:0055085 - transmembrane transport
GO:0071288 - cellular response to mercury ion
Note(s): Note(s): ...[more].
Reference(s): [1] Berendsen HJ. 2001
[2] Berman-Kurtz M., et al., 1971
[3] Bill RM., et al., 2001
[4] Calamita G., et al., 1995
[5] Chakrabarti N., et al., 2004
[6] Chen H., et al., 2007
[7] Chen LY. 2010
[8] Chen LY. 2013
[9] Cymer F., et al., 2010
[10] Duchesne L., et al., 2002
[11] Eze MO., et al., 1978
[12] Froger A., et al., 2001
[13] Galka JJ., et al., 2008
[14] Grayson P., et al., 2003
[15] Henin J., et al., 2008
[16] Hubert JF., et al., 2005
[17] Ilan B., et al., 2004
[18] Jensen MO., et al., 2006
[19] Jensen MO., et al., 2002
[20] Jensen MO., et al., 2005
[21] Klein N., et al., 2015
[22] Klein N., et al., 2019
[23] Kosztin I., et al., 2004
[24] Lin EC. 1986
[25] Liu Z., et al., 2006
[26] Lupski JR., et al., 1990
[27] Manley D., et al., 2003
[28] Manley DM., et al., 2000
[29] Neophytou I., et al., 2007
[30] Patargias G., et al., 2005
[31] Porquet A., et al., 2007
[32] Saparov SM., et al., 2005
[33] Schlick T. 2003
[34] Thomas D., et al., 2002
[35] Trefz M., et al., 2018
[36] Truniger V., et al., 1993
[37] Truniger V., et al., 1992
[38] Veerappan A., et al., 2011
[39] Wang Y., et al., 2005
[40] Zhu F., et al., 2002
External database links:  
DIP:
 DIP-47976N
ECOCYC:
 GLPF-MONOMER
ECOLIWIKI:
 b3927
INTERPRO:
 IPR000425
INTERPRO:
 IPR023271
INTERPRO:
 IPR022357
MODBASE:
 P0AER0
PDB:
 1LDI
PDB:
 1FX8
PDB:
 1LDA
PDB:
 1LDF
PFAM:
 PF00230
PRIDE:
 P0AER0
PRINTS:
 PR00783
PRODB:
 PRO_000022797
PROSITE:
 PS00221
REFSEQ:
 NP_418362
SMR:
 P0AER0
SWISSMODEL:
 P0AER0
UNIPROT:
 P0AER0


Operon      
Name: glpFKX         
Operon arrangement:
Transcription unit        Promoter
glpFKX


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


Regulation by small RNA    
  Display Regulation
small RNA spf


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 zapBp1 4118386 forward nd [ICWHO] [41]
  promoter TSS_4624 4118427 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4625 (cluster) 4118444 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4626 4118479 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4627 4118484 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4628 (cluster) 4118502 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4629 4118519 forward nd [RS-EPT-CBR] [42]
  promoter TSS_4630 (cluster) 4118531 forward nd [RS-EPT-CBR] [42]


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] Berendsen HJ., 2001, Bioinformatics. Reality simulation--observe while it happens., Science 294(5550):2304-5

 [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] Bill RM., Hedfalk K., Karlgren S., Mullins JG., Rydstrom J., Hohmann S., 2001, Analysis of the pore of the unusual major intrinsic protein channel, yeast Fps1p., J Biol Chem 276(39):36543-9

 [4] Calamita G., Bishai WR., Preston GM., Guggino WB., Agre P., 1995, Molecular cloning and characterization of AqpZ, a water channel from Escherichia coli., J Biol Chem 270(49):29063-6

 [5] Chakrabarti N., Roux B., Pomes R., 2004, Structural determinants of proton blockage in aquaporins., J Mol Biol 343(2):493-510

 [6] Chen H., Ilan B., Wu Y., Zhu F., Schulten K., Voth GA., 2007, Charge delocalization in proton channels, I: the aquaporin channels and proton blockage., Biophys J 92(1):46-60

 [7] Chen LY., 2010, Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations., Biophys Chem 151(3):178-80

 [8] Chen LY., 2013, Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF., Biochim Biophys Acta 1828(8):1786-93

 [9] Cymer F., Schneider D., 2010, A single glutamate residue controls the oligomerization, function, and stability of the aquaglyceroporin GlpF., Biochemistry 49(2):279-86

 [10] Duchesne L., Pellerin I., Delamarche C., Deschamps S., Lagree V., Froger A., Bonnec G., Thomas D., Hubert JF., 2002, Role of C-terminal domain and transmembrane helices 5 and 6 in function and quaternary structure of major intrinsic proteins: analysis of aquaporin/glycerol facilitator chimeric proteins., J Biol Chem 277(23):20598-604

 [11] Eze MO., McElhaney RN., 1978, Stopped-flow spectrophotometric assay of glycerol permeation in Escherichia coli: applicability and limitations., J Gen Microbiol 105(2):233-42

 [12] Froger A., Rolland JP., Bron P., Lagree V., Le Caherec F., Deschamps S., Hubert JF., Pellerin I., Thomas D., Delamarche C., 2001, Functional characterization of a microbial aquaglyceroporin., Microbiology 147(Pt 5):1129-35

 [13] Galka JJ., Baturin SJ., Manley DM., Kehler AJ., O'Neil JD., 2008, Stability of the glycerol facilitator in detergent solutions., Biochemistry 47(11):3513-24

 [14] Grayson P., Tajkhorshid E., Schulten K., 2003, Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics., Biophys J 85(1):36-48

 [15] Henin J., Tajkhorshid E., Schulten K., Chipot C., 2008, Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF., Biophys J 94(3):832-9

 [16] Hubert JF., Duchesne L., Delamarche C., Vaysse A., Gueune H., Raguenes-Nicol C., 2005, Pore selectivity analysis of an aquaglyceroporin by stopped-flow spectrophotometry on bacterial cell suspensions., Biol Cell 97(9):675-86

 [17] Ilan B., Tajkhorshid E., Schulten K., Voth GA., 2004, The mechanism of proton exclusion in aquaporin channels., Proteins 55(2):223-8

 [18] Jensen MO., Mouritsen OG., 2006, Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF., Biophys J 90(7):2270-84

 [19] Jensen MO., Park S., Tajkhorshid E., Schulten K., 2002, Energetics of glycerol conduction through aquaglyceroporin GlpF., Proc Natl Acad Sci U S A 99(10):6731-6

 [20] Jensen MO., Rothlisberger U., Rovira C., 2005, Hydroxide and proton migration in aquaporins., Biophys J 89(3):1744-59

 [21] Klein N., Hellmann N., Schneider D., 2015, Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF., Biophys J 109(4):722-31

 [22] Klein N., Trefz M., Schneider D., 2019, Covalently Linking Oligomerization-Impaired GlpF Protomers Does Not Completely Re-establish Wild-Type Channel Activity., Int J Mol Sci 20(4)

 [23] Kosztin I., Schulten K., 2004, Fluctuation-driven molecular transport through an asymmetric membrane channel., Phys Rev Lett 93(23):238102

 [24] Lin EC., 1986, Glycerol facilitator in Escherichia coli., Methods Enzymol 125:467-73

 [25] Liu Z., Styblo M., Rosen BP., 2006, Methylarsonous acid transport by aquaglyceroporins., Environ Health Perspect 114(4):527-31

 [26] 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

 [27] Manley D., O'Neil JD., 2003, Preparation of glycerol facilitator for protein structure and folding studies in solution., Methods Mol Biol 228:89-101

 [28] Manley DM., McComb ME., Perreault H., Donald LJ., Duckworth HW., O'Neil JD., 2000, Secondary structure and oligomerization of the E. coli glycerol facilitator., Biochemistry 39(40):12303-11

 [29] Neophytou I., Harvey R., Lawrence J., Marsh P., Panaretou B., Barlow D., 2007, Eukaryotic integral membrane protein expression utilizing the Escherichia coli glycerol-conducting channel protein (GlpF)., Appl Microbiol Biotechnol 77(2):375-381

 [30] Patargias G., Bond PJ., Deol SS., Sansom MS., 2005, Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment., J Phys Chem B 109(1):575-82

 [31] Porquet A., Filella M., 2007, Structural evidence of the similarity of Sb(OH)3 and As(OH)3 with glycerol: implications for their uptake., Chem Res Toxicol 20(9):1269-76

 [32] Saparov SM., Tsunoda SP., Pohl P., 2005, Proton exclusion by an aquaglyceroprotein: a voltage clamp study., Biol Cell 97(7):545-50

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

 [34] Thomas D., Bron P., Ranchy G., Duchesne L., Cavalier A., Rolland JP., Raguenes-Nicol C., Hubert JF., Haase W., Delamarche C., 2002, Aquaglyceroporins, one channel for two molecules., Biochim Biophys Acta 1555(1-3):181-6

 [35] Trefz M., Keller R., Vogt M., Schneider D., 2018, The GlpF residue Trp219 is part of an amino-acid cluster crucial for aquaglyceroporin oligomerization and function., Biochim Biophys Acta Biomembr 1860(4):887-894

 [36] Truniger V., Boos W., 1993, Glycerol uptake in Escherichia coli is sensitive to membrane lipid composition., Res Microbiol 144(7):565-74

 [37] Truniger V., Boos W., Sweet G., 1992, Molecular analysis of the glpFKX regions of Escherichia coli and Shigella flexneri., J Bacteriol 174(21):6981-91

 [38] Veerappan A., Cymer F., Klein N., Schneider D., 2011, The tetrameric α-helical membrane protein GlpF unfolds via a dimeric folding intermediate., Biochemistry 50(47):10223-30

 [39] Wang Y., Schulten K., Tajkhorshid E., 2005, What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF., Structure 13(8):1107-18

 [40] Zhu F., Tajkhorshid E., Schulten K., 2002, Pressure-induced water transport in membrane channels studied by molecular dynamics., Biophys J 83(1):154-60

 [41] 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

 [42] 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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