RegulonDB RegulonDB 10.9: Gene Form
   

xthA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

astC xthA ydjX astA NtrC NtrC NtrC ArgR ArgR ArgR ArgR terminator anti-terminator anti-anti-terminator TSS_2058 TSS_2058 TSS_2057 TSS_2057 TSS_2056 TSS_2056 ydjXp1 ydjXp1 ydjXp5 ydjXp5 xthAp xthAp astCp2 astCp2 astCp3 astCp3 astCp1 astCp1

Gene      
Name: xthA    Texpresso search in the literature
Synonym(s): ECK1747, EG11073, b1749, xth
Genome position(nucleotides): 1832428 --> 1833234 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.41
External database links:  
ASAP:
ABE-0005829
CGSC:
7
ECHOBASE:
EB1066
ECOLIHUB:
xthA
OU-MICROARRAY:
b1749
STRING:
511145.b1749
COLOMBOS: xthA


Product      
Name: exodeoxyribonuclease III
Synonym(s): Endonuclease VI, Xth, XthA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.969
Isoelectric point: 6.109
Motif(s):
 
Type Positions Sequence
4 -> 259 VSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYHGQKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCVETGIDYEIRSMEKPSDH
49 -> 50 KL

 

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:0003677 - DNA binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0004527 - exonuclease activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008853 - exodeoxyribonuclease III activity
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Centore RC., et al., 2008
[2] Chaudhry MA., et al., 1997
[3] Cunningham RP., et al., 1986
[4] Daley JM., et al., 2010
[5] Demple B., et al., 1986
[6] Gossard F., et al., 1978
[7] Greenberg MM., et al., 2004
[8] Hoheisel JD. 1993
[9] Kaluz S., et al., 1992
[10] Kirtikar DM., et al., 1976
[11] Kirtikar DM., et al., 1977
[12] Kow YW. 1989
[13] Kow YW., et al., 1985
[14] Kuo CF., et al., 1993
[15] Kuo CF., et al., 1994
[16] Kurita H., et al., 2008
[17] Linxweiler W., et al., 1982
[18] Mazouzi A., et al., 2013
[19] Milcarek C., et al., 1972
[20] Milcarek C., et al., 1973
[21] Mol CD., et al., 1995
[22] Nozaki S., et al., 2019
[23] Richardson CC., et al., 1964
[24] Richardson CC., et al., 1964
[25] Rogers SG., et al., 1980
[26] Rogers SG., et al., 1980
[27] Roychoudhury R., et al., 1977
[28] Sak BD., et al., 1989
[29] Sammartano LJ., et al., 1983
[30] Saporito SM., et al., 1988
[31] Shida T., et al., 1999
[32] Shida T., et al., 1995
[33] Shida T., et al., 1996
[34] Souza LL., et al., 2006
[35] Takeuchi M., et al., 1994
[36] Taylor AF., et al., 1982
[37] Watanabe K., et al., 2016
[38] Weiss B. 1976
[39] Weiss B. 1976
[40] White BJ., et al., 1976
[41] Yajko DM., et al., 1975
External database links:  
DIP:
DIP-11148N
ECOCYC:
EG11073-MONOMER
ECOLIWIKI:
b1749
INTERPRO:
IPR004808
INTERPRO:
IPR036691
INTERPRO:
IPR037493
INTERPRO:
IPR005135
INTERPRO:
IPR020847
INTERPRO:
IPR020848
MODBASE:
P09030
PANTHER:
PTHR43250
PDB:
1AKO
PFAM:
PF03372
PRIDE:
P09030
PRODB:
PRO_000024239
PROSITE:
PS00726
PROSITE:
PS51435
PROSITE:
PS00728
PROSITE:
PS00727
REFSEQ:
NP_416263
SMR:
P09030
UNIPROT:
P09030


Operon      
Name: xthA         
Operon arrangement:
Transcription unit        Promoter
xthA


RNA cis-regulatory element    
Attenuation: Transcriptional


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 ydjXp5 1833217 forward Similarity to the consensus
Read more >
[ICWHO] [42]
  promoter ydjXp1 1833308 forward Similarity to the consensus
Read more >
[ICWHO] [42]
  promoter TSS_2056 1833345 forward nd [RS-EPT-CBR] [43]
  promoter TSS_2057 1833569 forward nd [RS-EPT-CBR] [43]
  promoter TSS_2058 1833986 forward nd [RS-EPT-CBR] [43]


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] Centore RC., Lestini R., Sandler SJ., 2008, XthA (Exonuclease III) regulates loading of RecA onto DNA substrates in log phase Escherichia coli cells., Mol Microbiol 67(1):88-101

 [2] Chaudhry MA., Weinfeld M., 1997, Reactivity of human apurinic/apyrimidinic endonuclease and Escherichia coli exonuclease III with bistranded abasic sites in DNA., J Biol Chem 272(25):15650-5

 [3] Cunningham RP., Saporito SM., Spitzer SG., Weiss B., 1986, Endonuclease IV (nfo) mutant of Escherichia coli., J Bacteriol 168(3):1120-7

 [4] Daley JM., Zakaria C., Ramotar D., 2010, The endonuclease IV family of apurinic/apyrimidinic endonucleases., Mutat Res 705(3):217-27

 [5] Demple B., Johnson A., Fung D., 1986, Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli., Proc Natl Acad Sci U S A 83(20):7731-5

 [6] Gossard F., Verly WG., 1978, Properties of the main endonuclease specific for apurinic sites of Escherichia coli (endonuclease VI). Mechanism of apurinic site excision from DNA., Eur J Biochem 82(2):321-32

 [7] Greenberg MM., Weledji YN., Kim J., Bales BC., 2004, Repair of oxidized abasic sites by exonuclease III, endonuclease IV, and endonuclease III., Biochemistry 43(25):8178-83

 [8] Hoheisel JD., 1993, On the activities of Escherichia coli exonuclease III., Anal Biochem 209(2):238-46

 [9] Kaluz S., Kolble K., Reid KB., 1992, Directional cloning of PCR products using exonuclease III., Nucleic Acids Res 20(16):4369-70

 [10] Kirtikar DM., Cathcart GR., Goldthwait DA., 1976, Endonuclease II, apurinic acid endonuclease, and exonuclease III., Proc Natl Acad Sci U S A 73(12):4324-8

 [11] Kirtikar DM., Cathcart GR., White JG., Ukstins I., Goldthwait DA., 1977, Mutations in Escherichia coli altering an apurinic endonuclease, endonuclease II, and exonuclease III and their effect on in vivo sensitivity to methylmethanesulfonate., Biochemistry 16(25):5625-31

 [12] Kow YW., 1989, Mechanism of action of Escherichia coli exonuclease III., Biochemistry 28(8):3280-7

 [13] Kow YW., Wallace SS., 1985, Exonuclease III recognizes urea residues in oxidized DNA., Proc Natl Acad Sci U S A 82(24):8354-8

 [14] Kuo CF., McRee DE., Cunningham RP., Tainer JA., 1993, Purification, crystallization and space group determination of DNA repair enzyme exonuclease III from E. coli., J Mol Biol 229(1):239-42

 [15] Kuo CF., Mol CD., Thayer MM., Cunningham RP., Tainer JA., 1994, Structure and function of the DNA repair enzyme exonuclease III from E. coli., Ann N Y Acad Sci 726:223-34: discussion 234-5

 [16] Kurita H., Inaishi K., Torii K., Urisu M., Nakano M., Katsura S., Mizuno A., 2008, Real-time direct observation of single-molecule DNA hydrolysis by exonuclease III., J Biomol Struct Dyn 25(5):473-80

 [17] Linxweiler W., Horz W., 1982, Sequence specificity of exonuclease III from E. coli., Nucleic Acids Res 10(16):4845-59

 [18] Mazouzi A., Vigouroux A., Aikeshev B., Brooks PJ., Saparbaev MK., Morera S., Ishchenko AA., 2013, Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases., Proc Natl Acad Sci U S A 110(33):E3071-80

 [19] Milcarek C., Weiss B., 1972, Mutants of Escherichia coli with altered deoxyribonucleases. I. Isolation and characterization of mutants for exonuclease 3., J Mol Biol 68(2):303-18

 [20] Milcarek C., Weiss B., 1973, Preliminary mapping of mutations affecting exonuclease 3 in Escherichia coli K-12., J Bacteriol 113(2):1086-8

 [21] Mol CD., Kuo CF., Thayer MM., Cunningham RP., Tainer JA., 1995, Structure and function of the multifunctional DNA-repair enzyme exonuclease III., Nature 374(6520):381-6

 [22] Nozaki S., Niki H., 2019, Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends., J Bacteriol 201(5)

 [23] Richardson CC., Kornberg A., 1964, A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli. I. Purification of the enzyme and characterization of the phosphatase activity., J Biol Chem 239:242-50

 [24] Richardson CC., Lehman IR., Kornberg A., 1964, A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli. II. Characterization of the exonuclease activity., J Biol Chem 239:251-8

 [25] Rogers SG., Weiss B., 1980, Exonuclease III of Escherichia coli K-12, an AP endonuclease., Methods Enzymol 65(1):201-11

 [26] Rogers SG., Weiss B., 1980, Cloning of the exonuclease III gene of Escherichia coli., Gene 11(3-4):187-95

 [27] Roychoudhury R., Wu R., 1977, Novel properties of Escherichia coli exonuclease III., J Biol Chem 252(14):4786-9

 [28] Sak BD., Eisenstark A., Touati D., 1989, Exonuclease III and the catalase hydroperoxidase II in Escherichia coli are both regulated by the katF gene product., Proc Natl Acad Sci U S A 86(9):3271-5

 [29] Sammartano LJ., Tuveson RW., 1983, Escherichia coli xthA mutants are sensitive to inactivation by broad-spectrum near-UV (300- to 400-nm) radiation., J Bacteriol 156(2):904-6

 [30] Saporito SM., Smith-White BJ., Cunningham RP., 1988, Nucleotide sequence of the xth gene of Escherichia coli K-12., J Bacteriol 170(10):4542-7

 [31] Shida T., Kaneda K., Ogawa T., Sekiguchi J., 1999, Abasic site recognition mechanism by the Escherichia coli exonuclease III., Nucleic Acids Symp Ser (42):195-6

 [32] Shida T., Noda M., Sekiguchi J., 1995, The recognition of DNA containing an AP site by E.coli endonuclease VI (exonuclease III)., Nucleic Acids Symp Ser (34):87-8

 [33] Shida T., Noda M., Sekiguchi J., 1996, Cleavage of single- and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI)., Nucleic Acids Res 24(22):4572-6

 [34] Souza LL., Eduardo IR., Padula M., Leitao AC., 2006, Endonuclease IV and exonuclease III are involved in the repair and mutagenesis of DNA lesions induced by UVB in Escherichia coli., Mutagenesis 21(2):125-30

 [35] Takeuchi M., Lillis R., Demple B., Takeshita M., 1994, Interactions of Escherichia coli endonuclease IV and exonuclease III with abasic sites in DNA., J Biol Chem 269(34):21907-14

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

 [37] Watanabe K., Tominaga K., Kitamura M., Kato JI., 2016, Systematic identification of synthetic lethal mutations with reduced-genome Escherichia coli: synthetic genetic interactions among yoaA, xthA and holC related to survival from MMS exposure., Genes Genet Syst 91(3):183-188

 [38] Weiss B., 1976, Endonuclease II of Escherichia coli is exonuclease III., J Biol Chem 251(7):1896-901

 [39] Weiss B., 1976, Terminal cross-linking of DNA strands by a mixture of exonuclease III of Escherichia coli and polynucleotide ligase of bacteriophage T4., J Mol Biol 103(3):669-73

 [40] White BJ., Hochhauser SJ., Cintron NM., Weiss B., 1976, Genetic mapping of xthA, the structural gene for exonuclease III in Escherichia coli K-12., J Bacteriol 126(3):1082-8

 [41] Yajko DM., Weiss B., 1975, Mutations simultaneously affecting endonuclease II and exonuclease III in Escherichia coli., Proc Natl Acad Sci U S A 72(2):688-92

 [42] 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

 [43] 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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