RegulonDB RegulonDB 10.10: Gene Form
   

ung gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yfiF ung grcA Fis CpxR Fis ArcA FNR ArcA FNR CRP Fis PdhR ungp ungp TSS_2888 TSS_2888 TSS_2887 TSS_2887 grcAp1 grcAp1 TSS_2886 (cluster) TSS_2886 (cluster) TSS_2885 (cluster) TSS_2885 (cluster) grcAp2 grcAp2 TSS_2884 (cluster) TSS_2884 (cluster) TSS_2883 TSS_2883 TSS_2882 TSS_2882 TSS_2881 TSS_2881 TSS_2880 TSS_2880 TSS_2879 (cluster) TSS_2879 (cluster) TSS_2878 (cluster) TSS_2878 (cluster) TSS_2877 TSS_2877 TSS_2876 TSS_2876 TSS_2875 TSS_2875

Gene      
Name: ung    Texpresso search in the literature
Synonym(s): ECK2578, EG11058, b2580
Genome position(nucleotides): 2716754 --> 2717443 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.17
External database links:  
ASAP:
ABE-0008495
CGSC:
25
ECHOBASE:
EB1051
ECOLIHUB:
ung
MIM:
608106
OU-MICROARRAY:
b2580
STRING:
511145.b2580
COLOMBOS: ung


Product      
Name: uracil-DNA glycosylase
Synonym(s): Ung, uracil-DNA glycosidase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 25.693
Isoelectric point: 7.22
Motif(s):
 
Type Positions Sequence
187 -> 187 H
55 -> 209 DVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQW
2 -> 229 ANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0004844 - uracil DNA N-glycosylase activity
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006284 - base-excision repair
GO:0097510 - base-excision repair, AP site formation via deaminated base removal
Note(s): Note(s): ...[more].
Reference(s): [1] Bennett SE., et al., 1994
[2] Bharti SK., et al., 2010
[3] D'souza DI., et al., 2003
[4] Delort AM., et al., 1985
[5] Duncan BK. 1985
[6] Duncan BK., et al., 1984
[7] Duncan BK., et al., 1980
[8] Fix DF., et al., 1990
[9] Handa P., et al., 2002
[10] Hayakawa H., et al., 1978
[11] Jiang YL., et al., 2002
[12] Kimber ST., et al., 2014
[13] Kumar NV., et al., 1994
[14] Kumar NV., et al., 1997
[15] Kwon K., et al., 2003
[16] Lari SU., et al., 2006
[17] Liu P., et al., 2002
[18] Lundquist AJ., et al., 1997
[19] Mechetin GV., et al., 2011
[20] Nilsen H., et al., 1995
[21] Olsen LC., et al., 1991
[22] Parker JB., et al., 2008
[23] Postel EH., et al., 2003
[24] Purmal AA., et al., 1996
[25] Sandigursky M., et al., 1998
[26] Seibert E., et al., 2002
[27] Shroyer MJ., et al., 1999
[28] Spek EJ., et al., 2002
[29] Sung JS., et al., 2001
[30] Sung JS., et al., 2003
[31] Taylor AF., et al., 1982
[32] Tye BK., et al., 1977
[33] Varshney U., et al., 1991
[34] Verri A., et al., 1992
[35] Warner HR., et al., 1981
[36] Werner RM., et al., 2000
[37] Werner RM., et al., 2000
[38] Yang Y., et al., 2019
External database links:  
DIP:
DIP-11092N
ECOCYC:
EG11058-MONOMER
ECOLIWIKI:
b2580
INTERPRO:
IPR002043
INTERPRO:
IPR036895
INTERPRO:
IPR005122
INTERPRO:
IPR018085
MODBASE:
P12295
PANTHER:
PTHR11264
PDB:
1EUI
PDB:
5EUG
PDB:
4EUG
PDB:
3UF7
PDB:
3EUG
PDB:
2UUG
PDB:
2EUG
PDB:
1EUG
PDB:
1FLZ
PDB:
1LQG
PDB:
1LQJ
PDB:
1LQM
PDB:
1UUG
PFAM:
PF03167
PRIDE:
P12295
PROSITE:
PS00130
REFSEQ:
NP_417075
SMART:
SM00986
SMR:
P12295
UNIPROT:
P12295


Operon      
Name: ung         
Operon arrangement:
Transcription unit        Promoter
ung


Transcriptional Regulation      
Display Regulation             
Repressed by: CpxR


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_2875 2716280 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2876 2716282 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2877 2716291 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2878 (cluster) 2716431 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2879 (cluster) 2716446 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2880 2716470 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2881 2716473 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2882 2716478 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2883 2716482 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2884 (cluster) 2716501 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2885 (cluster) 2716511 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2886 (cluster) 2716522 reverse nd [RS-EPT-CBR] [39]
  promoter TSS_2887 2716686 forward nd [RS-EPT-CBR] [39]
  promoter TSS_2888 2716730 forward nd [RS-EPT-CBR] [39]


Evidence    

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



Reference(s)    

 [1] Bennett SE., Jensen ON., Barofsky DF., Mosbaugh DW., 1994, UV-catalyzed cross-linking of Escherichia coli uracil-DNA glycosylase to DNA. Identification of amino acid residues in the single-stranded DNA binding site., J Biol Chem 269(34):21870-9

 [2] Bharti SK., Varshney U., 2010, Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli., Nucleic Acids Res 38(7):2291-301

 [3] D'souza DI., Harrison L., 2003, Repair of clustered uracil DNA damages in Escherichia coli., Nucleic Acids Res 31(15):4573-81

 [4] Delort AM., Duplaa AM., Molko D., Teoule R., Leblanc JP., Laval J., 1985, Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases., Nucleic Acids Res 13(2):319-35

 [5] Duncan BK., 1985, Isolation of insertion, deletion, and nonsense mutations of the uracil-DNA glycosylase (ung) gene of Escherichia coli K-12., J Bacteriol 164(2):689-95

 [6] Duncan BK., Chambers JA., 1984, The cloning and overproduction of Escherichia coli uracil-DNA glycosylase., Gene 28(2):211-9

 [7] Duncan BK., Miller JH., 1980, Mutagenic deamination of cytosine residues in DNA., Nature 287(5782):560-1

 [8] Fix DF., Koehler DR., Glickman BW., 1990, Uracil-DNA glycosylase activity affects the mutagenicity of ethyl methanesulfonate: evidence for an alternative pathway of alkylation mutagenesis., Mutat Res 244(2):115-21

 [9] Handa P., Acharya N., Varshney U., 2002, Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate., Nucleic Acids Res 30(14):3086-95

 [10] Hayakawa H., Kumura K., Sekiguchi M., 1978, Role of uracil-DNA glycosylase in the repair of deaminated cytosine residues of DNA in Escherichia coli., J Biochem 84(5):1155-64

 [11] Jiang YL., Ichikawa Y., Stivers JT., 2002, Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic., Biochemistry 41(22):7116-24

 [12] Kimber ST., Brown T., Fox KR., 2014, A mutant of uracil DNA glycosylase that distinguishes between cytosine and 5-methylcytosine., PLoS One 9(4):e95394

 [13] Kumar NV., Varshney U., 1994, Inefficient excision of uracil from loop regions of DNA oligomers by E. coli uracil DNA glycosylase., Nucleic Acids Res 22(18):3737-41

 [14] Kumar NV., Varshney U., 1997, Contrasting effects of single stranded DNA binding protein on the activity of uracil DNA glycosylase from Escherichia coli towards different DNA substrates., Nucleic Acids Res 25(12):2336-43

 [15] Kwon K., Jiang YL., Stivers JT., 2003, Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pyrene base pair., Chem Biol 10(4):351-9

 [16] Lari SU., Chen CY., Vertessy BG., Morre J., Bennett SE., 2006, Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance., DNA Repair (Amst) 5(12):1407-20

 [17] Liu P., Burdzy A., Sowers LC., 2002, Substrate recognition by a family of uracil-DNA glycosylases: UNG, MUG, and TDG., Chem Res Toxicol 15(8):1001-9

 [18] Lundquist AJ., Beger RD., Bennett SE., Bolton PH., Mosbaugh DW., 1997, Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein. Role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase., J Biol Chem 272(34):21408-19

 [19] Mechetin GV., Zharkov DO., 2011, Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions., Biochem Biophys Res Commun 414(2):425-30

 [20] Nilsen H., Yazdankhah SP., Eftedal I., Krokan HE., 1995, Sequence specificity for removal of uracil from U.A pairs and U.G mismatches by uracil-DNA glycosylase from Escherichia coli, and correlation with mutational hotspots., FEBS Lett 362(2):205-9

 [21] Olsen LC., Aasland R., Krokan HE., Helland DE., 1991, Human uracil-DNA glycosylase complements E. coli ung mutants., Nucleic Acids Res 19(16):4473-8

 [22] Parker JB., Stivers JT., 2008, Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions., Biochemistry 47(33):8614-22

 [23] Postel EH., Abramczyk BM., 2003, Escherichia coli nucleoside diphosphate kinase is a uracil-processing DNA repair nuclease., Proc Natl Acad Sci U S A 100(23):13247-52

 [24] Purmal AA., Rabow LE., Lampman GW., Cunningham RP., Kow YW., 1996, A common mechanism of action for the N-glycosylase activity of DNA N-glycosylase/AP lyases from E. coli and T4., Mutat Res 364(3):193-207

 [25] Sandigursky M., Freyer GA., Franklin WA., 1998, The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair., Nucleic Acids Res 26(5):1282-7

 [26] Seibert E., Ross JB., Osman R., 2002, Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase., Biochemistry 41(36):10976-84

 [27] Shroyer MJ., Bennett SE., Putnam CD., Tainer JA., Mosbaugh DW., 1999, Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis., Biochemistry 38(15):4834-45

 [28] Spek EJ., Vuong LN., Matsuguchi T., Marinus MG., Engelward BP., 2002, Nitric oxide-induced homologous recombination in Escherichia coli is promoted by DNA glycosylases., J Bacteriol 184(13):3501-7

 [29] Sung JS., Bennett SE., Mosbaugh DW., 2001, Fidelity of uracil-initiated base excision DNA repair in Escherichia coli cell extracts., J Biol Chem 276(3):2276-85

 [30] Sung JS., Mosbaugh DW., 2003, Escherichia coli uracil- and ethenocytosine-initiated base excision DNA repair: rate-limiting step and patch size distribution., Biochemistry 42(16):4613-25

 [31] Taylor AF., Weiss B., 1982, Role of exonuclease III in the base excision repair of uracil-containing DNA., J Bacteriol 151(1):351-7

 [32] Tye BK., Lehman IR., 1977, Excision repair of uracil incorporated in DNA as a result of a defect in dUTPase., J Mol Biol 117(2):293-306

 [33] Varshney U., van de Sande JH., 1991, Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase., Biochemistry 30(16):4055-61

 [34] Verri A., Mazzarello P., Spadari S., Focher F., 1992, Uracil-DNA glycosylases preferentially excise mispaired uracil., Biochem J 287 ( Pt 3):1007-10

 [35] Warner HR., Duncan BK., Garrett C., Neuhard J., 1981, Synthesis and metabolism of uracil-containing deoxyribonucleic acid in Escherichia coli., J Bacteriol 145(2):687-95

 [36] Werner RM., Jiang YL., Gordley RG., Jagadeesh GJ., Ladner JE., Xiao G., Tordova M., Gilliland GL., Stivers JT., 2000, Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase., Biochemistry 39(41):12585-94

 [37] Werner RM., Stivers JT., 2000, Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate., Biochemistry 39(46):14054-64

 [38] Yang Y., Park SH., Alford-Zappala M., Lee HW., Li J., Cunningham RP., Cao W., 2019, Role of endonuclease III enzymes in uracil repair., Mutat Res 813:20-30

 [39] 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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