RegulonDB

Gene
Name:	nei
Synonym(s):	ECK0703, G6383, b0714
Genome position(nucleotides):	745935 --> 746726 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.4
External database links:

ASAP:	ABE-0002433
ECHOBASE:	EB3026
OU-MICROARRAY:	b0714
PortEco:	nei
STRING:	511145.b0714
COLOMBOS:	nei

Gene

Name:

nei

Synonym(s):

ECK0703, G6383, b0714

Genome position(nucleotides):

745935 --> 746726 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.4

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

1 -> 104

MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLY

253 -> 253

262 -> 262

2 -> 263

PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH

235 -> 263

GEPCERCGSIIEKTTLSSRPFYWCPGCQH

Type

Positions

Sequence

1 -> 104

MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLY

253 -> 253

262 -> 262

2 -> 263

235 -> 263

GEPCERCGSIIEKTTLSSRPFYWCPGCQH

3 -> 3

6 -> 6

172 -> 172

129 -> 129

160 -> 160

174 -> 174

213 -> 213

127 -> 205

GPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEI

53 -> 53

229 -> 263

KVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH

Multifun Terms (GenProtEC)

2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol

molecular_function

GO:0140078 - class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
GO:0016829 - lyase activity
GO:0046872 - metal ion binding
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0003684 - damaged DNA binding
GO:0008270 - zinc ion binding
GO:0019104 - DNA N-glycosylase activity
GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0000703 - oxidized pyrimidine nucleobase lesion 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:0006289 - nucleotide-excision repair
GO:0090305 - nucleic acid phosphodiester bond hydrolysis

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_837	747325		reverse	nd	[RS-EPT-CBR]	[16]
	promoter	TSS_838	747803		reverse	nd	[RS-EPT-CBR]	[16]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_837

747325

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_838

747803

reverse

[RS-EPT-CBR]

[16]

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

Evidence

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

Reference(s)
[1] Blaisdell JO., Hatahet Z., Wallace SS., 1999, A novel role for Escherichia coli endonuclease VIII in prevention of spontaneous G-->T transversions., J Bacteriol 181(20):6396-402
[2] Burgess S., Jaruga P., Dodson ML., Dizdaroglu M., Lloyd RS., 2002, Determination of active site residues in Escherichia coli endonuclease VIII., J Biol Chem 277(4):2938-44
[3] 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
[4] 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
[5] Golan G., Zharkov DO., Fernandes AS., Zaika E., Kycia JH., Wawrzak Z., Grollman AP., Shoham G., 2004, Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form., Acta Crystallogr D Biol Crystallogr 60(Pt 8):1476-80
[6] 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
[7] Hazra TK., Izumi T., Venkataraman R., Kow YW., Dizdaroglu M., Mitra S., 2000, Characterization of a novel 8-oxoguanine-DNA glycosylase activity in Escherichia coli and identification of the enzyme as endonuclease VIII., J Biol Chem 275(36):27762-7
[8] Katafuchi A., Nakano T., Masaoka A., Terato H., Iwai S., Hanaoka F., Ide H., 2004, Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions., J Biol Chem 279(14):14464-71
[9] Lu AL., Lee CY., Li L., Li X., 2006, Physical and functional interactions between Escherichia coli MutY and endonuclease VIII., Biochem J 393(Pt 1):381-7
[10] Makasheva KA., Endutkin AV., Zharkov DO., 2019, Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases., Mutagenesis
[11] Rieger RA., McTigue MM., Kycia JH., Gerchman SE., Grollman AP., Iden CR., 2000, Characterization of a cross-linked DNA-endonuclease VIII repair complex by electrospray ionization mass spectrometry., J Am Soc Mass Spectrom 11(6):505-15
[12] 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
[13] 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
[14] Terato H., Masaoka A., Asagoshi K., Honsho A., Ohyama Y., Suzuki T., Yamada M., Makino K., Yamamoto K., Ide H., 2002, Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid., Nucleic Acids Res 30(22):4975-84
[15] 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
[16] 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.

Reference(s)

[1] Blaisdell JO., Hatahet Z., Wallace SS., 1999, A novel role for Escherichia coli endonuclease VIII in prevention of spontaneous G-->T transversions., J Bacteriol 181(20):6396-402

[2] Burgess S., Jaruga P., Dodson ML., Dizdaroglu M., Lloyd RS., 2002, Determination of active site residues in Escherichia coli endonuclease VIII., J Biol Chem 277(4):2938-44

[3] 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

[4] 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

[5] Golan G., Zharkov DO., Fernandes AS., Zaika E., Kycia JH., Wawrzak Z., Grollman AP., Shoham G., 2004, Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form., Acta Crystallogr D Biol Crystallogr 60(Pt 8):1476-80

[6] 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

[7] Hazra TK., Izumi T., Venkataraman R., Kow YW., Dizdaroglu M., Mitra S., 2000, Characterization of a novel 8-oxoguanine-DNA glycosylase activity in Escherichia coli and identification of the enzyme as endonuclease VIII., J Biol Chem 275(36):27762-7

[8] Katafuchi A., Nakano T., Masaoka A., Terato H., Iwai S., Hanaoka F., Ide H., 2004, Differential specificity of human and Escherichia coli endonuclease III and VIII homologues for oxidative base lesions., J Biol Chem 279(14):14464-71

[9] Lu AL., Lee CY., Li L., Li X., 2006, Physical and functional interactions between Escherichia coli MutY and endonuclease VIII., Biochem J 393(Pt 1):381-7

[10] Makasheva KA., Endutkin AV., Zharkov DO., 2019, Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases., Mutagenesis

[11] Rieger RA., McTigue MM., Kycia JH., Gerchman SE., Grollman AP., Iden CR., 2000, Characterization of a cross-linked DNA-endonuclease VIII repair complex by electrospray ionization mass spectrometry., J Am Soc Mass Spectrom 11(6):505-15

[12] 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

[13] 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

[14] Terato H., Masaoka A., Asagoshi K., Honsho A., Ohyama Y., Suzuki T., Yamada M., Makino K., Yamamoto K., Ide H., 2002, Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid., Nucleic Acids Res 30(22):4975-84

[15] 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

[16] 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.