RegulonDB RegulonDB 10.9: Gene Form
   

nth gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dtpA rsxE nth rsxG OmpR GadX anti-terminator anti-anti-terminator terminator TSS_1912 TSS_1912 TSS_1911 TSS_1911 tppBp tppBp TSS_1910 TSS_1910

Gene      
Name: nth    Texpresso search in the literature
Synonym(s): ECK1629, EG10662, b1633
Genome position(nucleotides): 1711523 --> 1712158 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.21
External database links:  
ASAP:
 ABE-0005463
CGSC:
 13070
ECHOBASE:
 EB0656
ECOLIHUB:
 nth
MIM:
 616415
OU-MICROARRAY:
 b1633
STRING:
 511145.b1633
COLOMBOS: nth


Product      
Name: endonuclease III
Synonym(s): Endo III, Nth
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 23.562
Isoelectric point: 8.287
Motif(s):
 
Type Positions Sequence
156 -> 166 VEQVEEKLLKV
61 -> 67 PAAMLEL
100 -> 127 HNGEVPEDRAALEALPGVGRKTANVVLN
107 -> 113 DRAALEA
119 -> 129 RKTANVVLNTA

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
  5 - cell processes --> 5.6 - protection --> 5.6.1 - radiation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0140078 - class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016829 - lyase activity
GO:0046872 - metal ion binding
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0019104 - DNA N-glycosylase activity
GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0000703 - oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
GO:0004844 - uracil DNA N-glycosylase activity
biological_process GO:0008152 - metabolic process
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006284 - base-excision repair
GO:0006285 - base-excision repair, AP site formation
GO:0034644 - cellular response to UV
GO:0097510 - base-excision repair, AP site formation via deaminated base removal
Note(s): Note(s): ...[more].
Reference(s): [1] Boal AK., et al., 2007
[2] Bricteux-Gregoire S., et al., 1989
[3] Chaudhry MA., et al., 1995
[4] Cronan GE., et al., 2019
[5] Cunningham RP., et al., 1989
[6] D'Ham C., et al., 1998
[7] David-Cordonnier MH., et al., 2001
[8] Denver DR., et al., 2003
[9] Dodson ML., et al., 1994
[10] Doi Y., et al., 2006
[11] Gifford CM., et al., 2000
[12] Grodick MA., et al., 2014
[13] Harrison L., et al., 1998
[14] Hazra TK., et al., 2001
[15] Hermans N., et al., 2016
[16] Hori M., et al., 2003
[17] Janion C., et al., 2003
[18] Jurado J., et al., 1998
[19] Kuznetsov NA., et al., 2015
[20] Laspia MF., et al., 1988
[21] Lomax ME., et al., 2005
[22] Matsumoto Y., et al., 2001
[23] Miller H., et al., 2004
[24] Piersen CE., et al., 2000
[25] Romano CA., et al., 2011
[26] Saito Y., et al., 1997
[27] Serafini DM., et al., 1999
[28] Sontz PA., et al., 2012
[29] Suzuki T., et al., 2008
[30] Tano K., et al., 2001
[31] Wagner JR., et al., 1996
[32] Watanabe T., et al., 2005
[33] Weiss B., et al., 1985
[34] Wiederholt CJ., et al., 2005
[35] Zhang QM., et al., 2000
External database links:  
DIP:
 DIP-48071N
ECOCYC:
 EG10662-MONOMER
ECOLIWIKI:
 b1633
INTERPRO:
 IPR003265
INTERPRO:
 IPR000445
INTERPRO:
 IPR023170
INTERPRO:
 IPR003651
INTERPRO:
 IPR004035
INTERPRO:
 IPR004036
INTERPRO:
 IPR005759
INTERPRO:
 IPR011257
MODBASE:
 P0AB83
PDB:
 2ABK
PFAM:
 PF00730
PFAM:
 PF00633
PFAM:
 PF10576
PRIDE:
 P0AB83
PRODB:
 PRO_000023419
PROSITE:
 PS00764
PROSITE:
 PS01155
REFSEQ:
 NP_416150
SMART:
 SM00525
SMART:
 SM00478
SMR:
 P0AB83
UNIPROT:
 P0AB83


Operon      
Name: ydgK-rsxABCDGE-nth         
Operon arrangement:
Transcription unit        Promoter
ydgK-rsxABCDGE-nth
rsxABCDGE-nth


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_1910 1711455 forward nd [RS-EPT-CBR] [36]
  promoter TSS_1911 1712673 forward nd [RS-EPT-CBR] [36]
  promoter TSS_1912 1713632 forward nd [RS-EPT-CBR] [36]


Evidence    

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


Reference(s)    

 [1] Boal AK., Yavin E., Barton JK., 2007, DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?, J Inorg Biochem 101(11-12):1913-21

 [2] Bricteux-Gregoire S., Verly WG., 1989, The use of thioglycolate to distinguish between 3' AP (apurinic/apyrimidinic) endonucleases and AP lyases., Nucleic Acids Res 17(15):6269-82

 [3] Chaudhry MA., Weinfeld M., 1995, The action of Escherichia coli endonuclease III on multiply damaged sites in DNA., J Mol Biol 249(5):914-22

 [4] Cronan GE., Kouzminova EA., Kuzminov A., 2019, Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision., Proc Natl Acad Sci U S A 116(4):1251-1260

 [5] Cunningham RP., Asahara H., Bank JF., Scholes CP., Salerno JC., Surerus K., Munck E., McCracken J., Peisach J., Emptage MH., 1989, Endonuclease III is an iron-sulfur protein., Biochemistry 28(10):4450-5

 [6] D'Ham C., Ravanat JL., Cadet J., 1998, Gas chromatography-mass spectrometry with high-performance liquid chromatography prepurification for monitoring the endonuclease III-mediated excision of 5-hydroxy-5,6-dihydrothymine and 5,6-dihydrothymine from gamma-irradiated DNA., J Chromatogr B Biomed Sci Appl 710(1-2):67-74

 [7] David-Cordonnier MH., Laval J., O'Neill P., 2001, Recognition and kinetics for excision of a base lesion within clustered DNA damage by the Escherichia coli proteins Fpg and Nth., Biochemistry 40(19):5738-46

 [8] Denver DR., Swenson SL., Lynch M., 2003, An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases., Mol Biol Evol 20(10):1603-11

 [9] Dodson ML., Michaels ML., Lloyd RS., 1994, Unified catalytic mechanism for DNA glycosylases., J Biol Chem 269(52):32709-12

 [10] Doi Y., Katafuchi A., Fujiwara Y., Hitomi K., Tainer JA., Ide H., Iwai S., 2006, Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction., Nucleic Acids Res 34(5):1540-51

 [11] Gifford CM., Wallace SS., 2000, The genes encoding endonuclease VIII and endonuclease III in Escherichia coli are transcribed as the terminal genes in operons., Nucleic Acids Res 28(3):762-9

 [12] Grodick MA., Segal HM., Zwang TJ., Barton JK., 2014, DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity., J Am Chem Soc 136(17):6470-8

 [13] Harrison L., Hatahet Z., Purmal AA., Wallace SS., 1998, Multiply damaged sites in DNA: interactions with Escherichia coli endonucleases III and VIII., Nucleic Acids Res 26(4):932-41

 [14] Hazra TK., Muller JG., Manuel RC., Burrows CJ., Lloyd RS., Mitra S., 2001, Repair of hydantoins, one electron oxidation product of 8-oxoguanine, by DNA glycosylases of Escherichia coli., Nucleic Acids Res 29(9):1967-74

 [15] Hermans N., Laffeber C., Cristovao M., Artola-Boran M., Mardenborough Y., Ikpa P., Jaddoe A., Winterwerp HH., Wyman C., Jiricny J., Kanaar R., Friedhoff P., Lebbink JH., 2016, Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair., Nucleic Acids Res 44(14):6770-86

 [16] Hori M., Yonei S., Sugiyama H., Kino K., Yamamoto K., Zhang QM., 2003, Identification of high excision capacity for 5-hydroxymethyluracil mispaired with guanine in DNA of Escherichia coli MutM, Nei and Nth DNA glycosylases., Nucleic Acids Res 31(4):1191-6

 [17] Janion C., Sikora A., Nowosielska A., Grzesiuk E., 2003, E. coli BW535, a triple mutant for the DNA repair genes xth, nth, and nfo, chronically induces the SOS response., Environ Mol Mutagen 41(4):237-42

 [18] Jurado J., Saparbaev M., Matray TJ., Greenberg MM., Laval J., 1998, The ring fragmentation product of thymidine C5-hydrate when present in DNA is repaired by the Escherichia coli Fpg and Nth proteins., Biochemistry 37(21):7757-63

 [19] Kuznetsov NA., Kladova OA., Kuznetsova AA., Ishchenko AA., Saparbaev MK., Zharkov DO., Fedorova OS., 2015, Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III., J Biol Chem

 [20] Laspia MF., Wallace SS., 1988, Excision repair of thymine glycols, urea residues, and apurinic sites in Escherichia coli., J Bacteriol 170(8):3359-66

 [21] Lomax ME., Salje H., Cunniffe S., O'Neill P., 2005, 8-OxoA inhibits the incision of an AP site by the DNA glycosylases Fpg, Nth and the AP endonuclease HAP1., Radiat Res 163(1):79-84

 [22] Matsumoto Y., Zhang QM., Takao M., Yasui A., Yonei S., 2001, Escherichia coli Nth and human hNTH1 DNA glycosylases are involved in removal of 8-oxoguanine from 8-oxoguanine/guanine mispairs in DNA., Nucleic Acids Res 29(9):1975-81

 [23] Miller H., Fernandes AS., Zaika E., McTigue MM., Torres MC., Wente M., Iden CR., Grollman AP., 2004, Stereoselective excision of thymine glycol from oxidatively damaged DNA., Nucleic Acids Res 32(1):338-45

 [24] Piersen CE., McCullough AK., Lloyd RS., 2000, AP lyases and dRPases: commonality of mechanism., Mutat Res 459(1):43-53

 [25] Romano CA., Sontz PA., Barton JK., 2011, Mutants of the base excision repair glycosylase, endonuclease III: DNA charge transport as a first step in lesion detection., Biochemistry 50(27):6133-45

 [26] Saito Y., Uraki F., Nakajima S., Asaeda A., Ono K., Kubo K., Yamamoto K., 1997, Characterization of endonuclease III (nth) and endonuclease VIII (nei) mutants of Escherichia coli K-12., J Bacteriol 179(11):3783-5

 [27] Serafini DM., Schellhorn HE., 1999, Endonuclease III and endonuclease IV protect Escherichia coli from the lethal and mutagenic effects of near-UV irradiation., Can J Microbiol 45(7):632-7

 [28] Sontz PA., Mui TP., Fuss JO., Tainer JA., Barton JK., 2012, DNA charge transport as a first step in coordinating the detection of lesions by repair proteins., Proc Natl Acad Sci U S A 109(6):1856-61

 [29] Suzuki T., Yamamoto K., Harashima H., Kamiya H., 2008, Base excision repair enzyme endonuclease III suppresses mutagenesis caused by 8-hydroxy-dGTP., DNA Repair (Amst) 7(1):88-94

 [30] Tano K., Iwamatsu Y., Yasuhira S., Utsumi H., Takimoto K., 2001, Increased base change mutations at G:C pairs in Escherichia coli deficient in endonuclease III and VIII., J Radiat Res 42(4):409-13

 [31] Wagner JR., Blount BC., Weinfeld M., 1996, Excision of oxidative cytosine modifications from gamma-irradiated DNA by Escherichia coli endonuclease III and human whole-cell extracts., Anal Biochem 233(1):76-86

 [32] Watanabe T., Blaisdell JO., Wallace SS., Bond JP., 2005, Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses., J Biol Chem 280(40):34378-84

 [33] Weiss B., Cunningham RP., 1985, Genetic mapping of nth, a gene affecting endonuclease III (thymine glycol-DNA glycosylase) in Escherichia coli K-12., J Bacteriol 162(2):607-10

 [34] Wiederholt CJ., Patro JN., Jiang YL., Haraguchi K., Greenberg MM., 2005, Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli., Nucleic Acids Res 33(10):3331-8

 [35] Zhang QM., Miyabe I., Matsumoto Y., Kino K., Sugiyama H., Yonei S., 2000, Identification of repair enzymes for 5-formyluracil in DNA. Nth, Nei, and MutM proteins of Escherichia coli., J Biol Chem 275(45):35471-7

 [36] 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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