RegulonDB RegulonDB 10.8: Gene Form
   

nei gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybgO abrB nei pxpA pxpC ybgP anti-terminator terminator TSS_838 TSS_838 TSS_837 TSS_837 neip neip

Gene      
Name: nei    Texpresso search in the literature
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


Product      
Name: endonuclease VIII
Synonym(s): Nei
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 29.845
Isoelectric point: 8.039
Motif(s):
 
Type Positions Sequence
1 -> 104 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLY
253 -> 253 R
262 -> 262 Q
2 -> 263 PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH
235 -> 263 GEPCERCGSIIEKTTLSSRPFYWCPGCQH

 

Classification:
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
Note(s): Note(s): ...[more].
Reference(s): [1] Blaisdell JO., et al., 1999
[2] Burgess S., et al., 2002
[3] Cronan GE., et al., 2019
[4] Gifford CM., et al., 2000
[5] Golan G., et al., 2004
[6] Harrison L., et al., 1998
[7] Hazra TK., et al., 2000
[8] Katafuchi A., et al., 2004
[9] Lu AL., et al., 2006
[10] Makasheva KA., et al., 2019
[11] Rieger RA., et al., 2000
[12] Saito Y., et al., 1997
[13] Tano K., et al., 2001
[14] Terato H., et al., 2002
[15] Wiederholt CJ., et al., 2005
External database links:  
DIP:
DIP-10327N
DISPROT:
DP00375
ECOCYC:
G6383-MONOMER
ECOLIWIKI:
b0714
INTERPRO:
IPR015886
INTERPRO:
IPR035937
INTERPRO:
IPR000214
INTERPRO:
IPR010663
INTERPRO:
IPR015887
INTERPRO:
IPR012319
INTERPRO:
IPR010979
INTERPRO:
IPR023713
MINT:
MINT-1221359
MODBASE:
P50465
PANTHER:
PTHR22993:SF14
PDB:
6FBU
PDB:
2OQ4
PDB:
2EA0
PDB:
1Q3C
PDB:
1Q3B
PDB:
1Q39
PDB:
1K3X
PDB:
1K3W
PDB:
2OPF
PFAM:
PF01149
PFAM:
PF06827
PFAM:
PF06831
PRIDE:
P50465
PRODB:
PRO_000023368
PROSITE:
PS51066
PROSITE:
PS51068
PROSITE:
PS01242
REFSEQ:
NP_415242
SMART:
SM00898
SMART:
SM01232
SMR:
P50465
UNIPROT:
P50465


Operon      
Name: ybgI-pxpBCA-nei         
Operon arrangement:
Transcription unit        Promoter
ybgIJKL-nei
ybgIJKL-nei
nei


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_837 747325 reverse nd [RS-EPT-CBR] [16]
  promoter TSS_838 747803 reverse nd [RS-EPT-CBR] [16]


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.


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