RegulonDB RegulonDB 10.9: Gene Form
   

glcD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

glcD glcF glcE glcC Fis GlcC Cra ArcA CRP IHF ArcA Fis PdhR Fis Fis glcCp glcCp glcDp glcDp TSS_3300 TSS_3300

Gene      
Name: glcD    Texpresso search in the literature
Synonym(s): ECK2974, G7545, b2979, gox, yghM
Genome position(nucleotides): 3126522 <-- 3128021 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.67
External database links:  
ASAP:
ABE-0009773
ECHOBASE:
EB2820
ECOLIHUB:
glcD
OU-MICROARRAY:
b2979
STRING:
511145.b2979
COLOMBOS: glcD


Shine dalgarno      
Sequence: cacaacaaagCGAAGCctactCAT


Product      
Name: glycolate dehydrogenase, putative FAD-linked subunit
Synonym(s): GlcD, Gox, YghM
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 53.812
Isoelectric point: 4.825
Motif(s):
 
Type Positions Sequence
56 -> 194 PLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTL
231 -> 470 PPVARVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPGVLEGIARLSQQYDLRVANVFHAGDGNMHPLILFDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVKAAFDPDGLLNPGK
52 -> 230 YRTRPLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTLGSDALDSPGFDLLALFTGSEGMLGVTTEVTVKLLPK

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.25 - glycolate metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0009339 - glycolate oxidase complex
molecular_function GO:0003824 - catalytic activity
GO:0016491 - oxidoreductase activity
GO:0019154 - glycolate dehydrogenase activity
GO:0050660 - flavin adenine dinucleotide binding
GO:0008891 - glycolate oxidase activity
GO:0071949 - FAD binding
biological_process GO:0006974 - cellular response to DNA damage stimulus
GO:0046296 - glycolate catabolic process
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Cabulong RB., et al., 2018
[2] Choi SY., et al., 2016
[3] Matsumoto K., et al., 2019
[4] Si HM., et al., 2016
[5] Sweeney J., et al., 2015
External database links:  
ECOCYC:
G7545-MONOMER
ECOLIWIKI:
b2979
INTERPRO:
IPR036318
INTERPRO:
IPR016171
INTERPRO:
IPR016166
INTERPRO:
IPR004113
INTERPRO:
IPR004490
INTERPRO:
IPR006094
INTERPRO:
IPR016164
MODBASE:
P0AEP9
PFAM:
PF02913
PFAM:
PF01565
PRIDE:
P0AEP9
PROSITE:
PS51387
REFSEQ:
NP_417453
UNIPROT:
P0AEP9


Operon      
Name: glcDEFGBA         
Operon arrangement:
Transcription unit        Promoter
glcDEFGBA
glcBA


Transcriptional Regulation      
Display Regulation             
Activated by: GlcC, IHF
Repressed by: ArcA, PdhR


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_3300 3124265 reverse nd [RS-EPT-CBR] [6]


Evidence    

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



Reference(s)    

 [1] Cabulong RB., Lee WK., Banares AB., Ramos KRM., Nisola GM., Valdehuesa KNG., Chung WJ., 2018, Engineering Escherichia coli for glycolic acid production from D-xylose through the Dahms pathway and glyoxylate bypass., Appl Microbiol Biotechnol 102(5):2179-2189

 [2] Choi SY., Park SJ., Kim WJ., Yang JE., Lee H., Shin J., Lee SY., 2016, One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli., Nat Biotechnol 34(4):435-40

 [3] Matsumoto K., Saito J., Yokoo T., Hori C., Nagata A., Kudoh Y., Ooi T., Taguchi S., 2019, Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-mediated de novo synthesis of glycolate-based polyhydroxyalkanoate in Escherichia coli., J Biosci Bioeng 128(3):302-306

 [4] Si HM., Zhang F., Wu AN., Han RZ., Xu GC., Ni Y., 2016, DNA microarray of global transcription factor mutant reveals membrane-related proteins involved in n-butanol tolerance in Escherichia coli., Biotechnol Biofuels 9:114

 [5] Sweeney J., Murphy CD., McDonnell K., 2015, Towards an effective biosensor for monitoring AD leachate: a knockout E. coli mutant that cannot catabolise lactate., Appl Microbiol Biotechnol 99(23):10209-14

 [6] 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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