RegulonDB RegulonDB 10.10: Gene Form
   

endA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rsmE endA yggI terminator TSS_3272 TSS_3272 TSS_3271 TSS_3271 TSS_3270 TSS_3270 rsmEp4 rsmEp4 rsmEp1 rsmEp1 endAp1 endAp1 endAp2 endAp2

Gene      
Name: endA    Texpresso search in the literature
Synonym(s): ECK2940, EG11336, b2945
Genome position(nucleotides): 3090347 --> 3091054 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.8
External database links:  
ASAP:
ABE-0009661
CGSC:
824
ECHOBASE:
EB1312
ECOLIHUB:
endA
OU-MICROARRAY:
b2945
STRING:
511145.b2945
COLOMBOS: endA


Shine dalgarno      
Sequence: gttttaacacGGAGTAagtgATG


Product      
Name: DNA-specific endonuclease I
Synonym(s): EndA
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 26.709
Isoelectric point: 9.326
Motif(s):
 
Type Positions Sequence
23 -> 235 EGINSFSQAKAAAVKVHADAPGTFYCGCKINWQGKKGVVDLQSCGYQVRKNENRASRVEWEHVVPAWQFGHQRQCWQDGGRKNCAKDPVYRKMESDMHNLQPSVGEVNGDRGNFMYSQWNGGEGQYGQCAMKVDFKEKAAEPPARARGAIARTYFYMRDQYNLTLSRQQTQLFNAWNKMYPVTDWECERDERIAKVQGNHNPYVQRACQARKS
42 -> 229 APGTFYCGCKINWQGKKGVVDLQSCGYQVRKNENRASRVEWEHVVPAWQFGHQRQCWQDGGRKNCAKDPVYRKMESDMHNLQPSVGEVNGDRGNFMYSQWNGGEGQYGQCAMKVDFKEKAAEPPARARGAIARTYFYMRDQYNLTLSRQQTQLFNAWNKMYPVTDWECERDERIAKVQGNHNPYVQRA
1 -> 22 MYRYLSIAAVVLSAAFSGPALA

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
GO:0004530 - deoxyribonuclease I activity
GO:0016888 - endodeoxyribonuclease activity, producing 5'-phosphomonoesters
biological_process GO:0006308 - DNA catabolic process
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Akaboshi E. 1999
[2] Akaboshi E. 2005
[3] Ananthaswamy HN. 1976
[4] Ananthaswamy HN. 1977
[5] Bernardi A., et al., 1975
[6] Bernardi G., et al., 1965
[7] Borja GM., et al., 2012
[8] Cherepanov PP., et al., 1995
[9] Cordonnier C., et al., 1965
[10] Eigner J., et al., 1968
[11] Goebel W., et al., 1970
[12] Griffith M., et al., 2003
[13] Jekel M., et al., 1994
[14] Khachatourians GG. 1979
[15] Lin JJ. 1992
[16] McIntosh MA., et al., 1975
[17] Molholt B., et al., 1968
[18] Richardson CC. 1966
[19] Taylor RG., et al., 1993
[20] Wnendt S. 1994
[21] Yau SY., et al., 2008
External database links:  
ECOCYC:
EG11336-MONOMER
ECOLIWIKI:
b2945
INTERPRO:
IPR007346
MODBASE:
P25736
PANTHER:
PTHR33607
PFAM:
PF04231
PRIDE:
P25736
PRODB:
PRO_000022515
REFSEQ:
NP_417420
SMR:
P25736
SWISSMODEL:
P25736
UNIPROT:
P25736


Operon      
Name: endA         
Operon arrangement:
Transcription unit        Promoter
endA
endA


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 rsmEp1 3091018 forward nd [ICWHO] [22]
  promoter rsmEp4 3091068 forward nd [ICWHO] [22]
  promoter TSS_3270 3091069 forward nd [RS-EPT-CBR] [23]
  promoter TSS_3271 3091787 forward nd [RS-EPT-CBR] [23]
  promoter TSS_3272 3091809 forward nd [RS-EPT-CBR] [23]


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] Akaboshi E., 1999, Recognition of sequence-directed structure of the ssDNA backbone by nucleases., Biochem Biophys Res Commun 256(3):532-6

 [2] Akaboshi E., 2005, Dynamic profiles of DNA: analysis of CAP- and LexA protein-binding regions with endonucleases., DNA Cell Biol 24(3):161-72

 [3] Ananthaswamy HN., 1976, The release of endonuclease I from Escherichia coli by a new cold shock procedure., Biochem Biophys Res Commun 76(2):289-98

 [4] Ananthaswamy HN., 1977, Release of periplasmic enzymes from Escherichia coli by penicillin-ethylenediaminetetraacetate treatment., J Bacteriol 131(2):710-2

 [5] Bernardi A., Gaillard C., Bernardi G., 1975, The specificity of five DNAases as studied by the analysis of 5'-terminal doublets., Eur J Biochem 52(3):451-7

 [6] Bernardi G., Cordonnier C., 1965, Mechanism of degradation of DNA by endonuclease I from Escherichia coli., J Mol Biol 11:141-3

 [7] Borja GM., Meza Mora E., Barron B., Gosset G., Ramirez OT., Lara AR., 2012, Engineering Escherichia coli to increase plasmid DNA production in high cell-density cultivations in batch mode., Microb Cell Fact 11:132

 [8] Cherepanov PP., Wackernagel W., 1995, Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant., Gene 158(1):9-14

 [9] Cordonnier C., Bernardi G., 1965, Localization of E. coli endonuclease I., Biochem Biophys Res Commun 20(5):555-9

 [10] Eigner J., Block S., 1968, Host-controlled restriction of T-even bacteriophages: relation of four bacterial deoxyribonucleases to restriction., J Virol 2(4):320-6

 [11] Goebel W., Helinski DR., 1970, Nicking activity of an endonuclease. I. Transfer ribonucleic acid complex of Escherichia coli., Biochemistry 9(24):4793-801

 [12] Griffith M., Gietz RD., 2003, Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection., Biotechniques 35(2):272-4, 276, 278

 [13] Jekel M., Wackernagel W., 1994, Location of the endA gene coding for endonuclease I on the physical map of the Escherichia coli K-12 chromosome., J Bacteriol 176(5):1550-1

 [14] Khachatourians GG., 1979, Escherichia coli Hfr-DNA degradation in endonuclease I-deficient minicells., Biochim Biophys Acta 561(2):294-300

 [15] Lin JJ., 1992, Endonuclease A degrades chromosomal and plasmid DNA of Escherichia coli present in most preparations of single stranded DNA from phagemids., Proc Natl Sci Counc Repub China B 16(1):1-5

 [16] McIntosh MA., Earhart CF., 1975, Effect of ribonuclease on the association of deoxyribonucleic acid with the membrane in Escherichia coli., J Bacteriol 122(2):592-8

 [17] Molholt B., Fraser D., 1968, Host-controlled restriction of T-even bacteriophages: relation of endonuclease I and T-even-induced nucleases to restriction., J Virol 2(4):313-9

 [18] Richardson CC., 1966, Influence of glucosylation of deoxyribonucleic acid on hydrolysis by deoxyribonucleases of Escherichia coli., J Biol Chem 241(9):2084-92

 [19] Taylor RG., Walker DC., McInnes RR., 1993, E. coli host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing., Nucleic Acids Res 21(7):1677-8

 [20] Wnendt S., 1994, Analysis of the endA mutation of Escherichia coli K12 strains: JM103 behaves like endA+ wild-type strains., Biotechniques 17(2):270, 272

 [21] Yau SY., Keshavarz-Moore E., Ward J., 2008, Host strain influences on supercoiled plasmid DNA production in Escherichia coli: Implications for efficient design of large-scale processes., Biotechnol Bioeng 101(3):529-44

 [22] 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

 [23] 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.


RegulonDB