RegulonDB RegulonDB 10.6.3: Gene Form
   

deoB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

deoA deoB deoD anti-terminator anti-anti-terminator terminator anti-terminator anti-anti-terminator TSS_5171 TSS_5171 TSS_5170 TSS_5170 TSS_5169 TSS_5169 TSS_5168 TSS_5168 TSS_5167 TSS_5167 TSS_5166 (cluster) TSS_5166 (cluster) deoBp deoBp

Gene      
Name: deoB    Texpresso search in the literature
Synonym(s): ECK4375, EG10220, b4383, drm, thyR, tlr
Genome position(nucleotides): 4619603 --> 4620826 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.33
External database links:  
ASAP:
ABE-0014377
CGSC:
867
ECHOBASE:
EB0216
ECOCYC:
EG10220
ECOLIHUB:
deoB
OU-MICROARRAY:
b4383
REGULONDB:
b4383
STRING:
511145.b4383
M3D: deoB
COLOMBOS: deoB
PortEco: b4383


Product      
Name: phosphopentomutase
Synonym(s): DeoB, Drm, ThyR, Tlr
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 44.37
Isoelectric point: 4.927
Motif(s):
 
Type Positions Sequence
2 -> 398 KRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLGLAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDHENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIACHEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAPTVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFTNFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHTREHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTS

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0008973 - phosphopentomutase activity
GO:0000287 - magnesium ion binding
GO:0030145 - manganese ion binding
biological_process GO:0009117 - nucleotide metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0043094 - cellular metabolic compound salvage
GO:0009166 - nucleotide catabolic process
GO:0009264 - deoxyribonucleotide catabolic process
GO:0006015 - 5-phosphoribose 1-diphosphate biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Ahmad SI., et al., 1979
[2] Ahmad SI., et al., 1969
[3] Albrechtsen H., et al., 1980
[4] Bonney RJ., et al., 1971
[5] Bonney RJ., et al., 1971
[6] Breitman TR., et al., 1968
[7] Buxton RS., et al., 1978
[8] Fateev IV., et al., 2014
[9] Fischer M., et al., 1982
[10] Hammer-Jespersen K., et al., 1976
[11] Hove-Jensen B., et al., 2003
[12] Sangurdekar DP., et al., 2011
[13] Skladnev DA., et al., 1978
[14] Sukhodolets VV. 1999
[15] Sukhodolets VV. 2000
[16] Sukhodolets VV. 2002
[17] Sukhodolets VV. 1997
[18] Sukhodolets VV. 1998
[19] Sukhodolets VV., et al., 2001
[20] Sukhodolets VV., et al., 1996
[21] Sukhodolets VV., et al., 2005
[22] Sukhodolets VV., et al., 2002
[23] Svenningsen BA. 1975
External database links:  
DIP:
DIP-48057N
ECOCYC:
PPENTOMUT-MONOMER
ECOLIWIKI:
b4383
INTERPRO:
IPR017849
INTERPRO:
IPR024052
INTERPRO:
IPR017850
INTERPRO:
IPR010045
INTERPRO:
IPR006124
MODBASE:
P0A6K6
PANTHER:
PTHR21110
PFAM:
PF01676
PRIDE:
P0A6K6
PRODB:
PRO_000022428
PROTEINMODELPORTAL:
P0A6K6
REFSEQ:
NP_418800
SMR:
P0A6K6
UNIPROT:
P0A6K6


Operon      
Name: deoCABD         
Operon arrangement:
Transcription unit        Promoter
deoCABD
deoCABD
deoBD
deoA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Fis
Repressed by: CRP, DeoR, ModE, CytR


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_5166 (cluster) 4619576 forward For this promoter, there
Read more >
[RS-EPT-CBR] [24]
  promoter TSS_5167 4619991 forward nd [RS-EPT-CBR] [24]
  promoter TSS_5168 4620783 forward nd [RS-EPT-CBR] [24]
  promoter TSS_5169 4620785 forward nd [RS-EPT-CBR] [24]
  promoter TSS_5170 4620789 forward nd [RS-EPT-CBR] [24]
  promoter TSS_5171 4621110 forward nd [RS-EPT-CBR] [24]


Evidence    

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



Reference(s)    

 [1] Ahmad SI., Eisenstark A., 1979, Thymidine sensitivity of certain strains of Escherichia coli K12., Mol Gen Genet 172(2):229-31

 [2] Ahmad SI., Pritchard RH., 1969, A map of four genes specifying enzymes involved in catabolism of nucleosides and deoxynucleosides in Escherichia coli., Mol Gen Genet 104(4):351-9

 [3] Albrechtsen H., Ahmad SI., 1980, Regulation of the synthesis of nucleoside catabolic enzymes in Escherichia coli: further analysis of a deo Oc mutant strain., Mol Gen Genet 179(2):457-60

 [4] Bonney RJ., Weinfeld H., 1971, Regulation of thymidine metabolism in Escherichia coli K-12: evidence that at least two operons control the degradation of thymidine., J Bacteriol 105(3):940-6

 [5] Bonney RJ., Weinfeld H., 1971, Regulation of thymidine metabolism in Escherichia coli K-12: studies on the inducer and the coordinateness of induction of the enzymes., J Bacteriol 106(3):812-8

 [6] Breitman TR., Bradford RM., 1968, Inability of low thymine-requiring mutants of Escherichia coli lacking phosphodeoxyribomutase to be induced for deoxythymidine phosphorylase and deoxyriboaldolase., J Bacteriol 95(6):2434-5

 [7] Buxton RS., Hammer-Jespersen K., Hansen TD., 1978, Insertion of bacteriophage lambda into the deo operon of Escherichia coli K-12 and isolation of plaque-forming lambdadeo+ transducing bacteriophages., J Bacteriol 136(2):668-81

 [8] Fateev IV., Antonov KV., Konstantinova ID., Muravyova TI., Seela F., Esipov RS., Miroshnikov AI., Mikhailopulo IA., 2014, The chemoenzymatic synthesis of clofarabine and related 2'-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases., Beilstein J Org Chem 10:1657-69

 [9] Fischer M., Short SA., 1982, The cloning of the Escherichia coli K-12 deoxyribonucleoside operon., Gene 17(3):291-8

 [10] Hammer-Jespersen K., Nygaard P., 1976, Multiple regulation of nucleoside catabolizing enzymes in Escherichia coli: effects of 3:5' cyclic AMP and CRP protein., Mol Gen Genet 148(1):49-55

 [11] Hove-Jensen B., Rosenkrantz TJ., Haldimann A., Wanner BL., 2003, Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways., J Bacteriol 185(9):2793-801

 [12] Sangurdekar DP., Zhang Z., Khodursky AB., 2011, The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim., BMC Genomics 12:583

 [13] Skladnev DA., Sukhodolets VV., Mironov AS., 1978, [Regulation of the activity of Escherichia coli deo-operon structural genes: the mutation mapped within the operon boundaries and affecting drm and pup gene activity]., Genetika 14(12):2091-101

 [14] Sukhodolets VV., 1999, [Formation of the heterozygous tandem duplication in the process of conjugation recombination in Escherichia coli: study of the effect of mutations for the recQ, uvrD, and recJ genes]., Genetika 35(4):450-8

 [15] Sukhodolets VV., 2000, [Homologous recombination between direct repeats of chromosomal segments comprising heterozygotic duplications in Escherichia coli]., Genetika 36(6):758-66

 [16] Sukhodolets VV., 2002, [Effect of mutations for the ruvABC genes on recombination between direct DNA repairs in Escherichia coli strains carrying extended tandem duplication]., Genetika 38(9):1215-22

 [17] Sukhodolets VV., 1997, [Genetic study of the mechanism of tandem duplication formation in conjugational crosses in Escherichia coli K-12]., Genetika 33(11):1487-93

 [18] Sukhodolets VV., 1998, [Further genetic study of tandem duplication formation in the region of the deo operon in the process of Escherichia coli K-12 conjugational recombination]., Genetika 34(10):1338-44

 [19] Sukhodolets VV., Botina SG., Trenina MA., Ukhabotina LS., 2001, [Homologous recombination and chromosomal rearrangements in Escherichia coli strains carrying a heterozygous tandem duplication]., Genetika 37(5):591-601

 [20] Sukhodolets VV., Dukhii DE., 1996, [Unequal crossing over in Escherichia coli: genetic and physical mapping of duplications isolated in conjugational matings]., Genetika 32(1):42-52

 [21] Sukhodolets VV., Prokop'ev VV., 2005, [Unequal genetic exchange in Escherichia coli tandem duplications may represent a special pathway of homologous recombination]., Genetika 41(3):307-11

 [22] Sukhodolets VV., Trenina MA., 2002, [Study of RecA-independent homologous recombination and a chromosomal rearrangement in the Escherichia coli strain carrying an extended tandem duplication]., Genetika 38(2):171-81

 [23] Svenningsen BA., 1975, Regulated in vitro synthesis of the enzymes of the deo operon of Escerichia coli. properties of the DNA directed system., Mol Gen Genet 137(4):289-304

 [24] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.


RegulonDB