RegulonDB RegulonDB 10.9: Gene Form
   

ybaZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybaY atl ffs terminator TSS_610 TSS_610 ffsp7 ffsp7 ffsp5 ffsp5 ffsp6 ffsp6

Gene      
Name: ybaZ    Texpresso search in the literature
Synonym(s): ECK0448, G6251, atl, b0454
Genome position(nucleotides): 475982 <-- 476371 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.1
External database links:  
ASAP:
ABE-0001576
ECHOBASE:
EB3043
ECOLIHUB:
atl
OU-MICROARRAY:
b0454
STRING:
511145.b0454
COLOMBOS: ybaZ


Product      
Name: DNA base-flipping protein
Synonym(s): Atl, YbaZ, alkyltransferase-like protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.45
Isoelectric point: 9.487
Motif(s):
 
Type Positions Sequence
33 -> 112 FPQRVWQIVAAIPEGYVTTYGDVAKLAGSPRAARQVGGVLKRLPEGSTLPWHRVVNRHGTISLTGPDLQRQRQALLAEGV
83 -> 83 W

 

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:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0003684 - damaged DNA binding
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
Note(s): Note(s): ...[more].
Evidence: [APPP] Assay of partially-purified protein
[IGI] Inferred from genetic interaction
Reference(s): [1] Chen CS., et al., 2008
[2] Mazon G., et al., 2009
[3] Mazon G., et al., 2010
[4] Tomaszowski KH., et al., 2015
External database links:  
DIP:
DIP-48135N
ECOCYC:
G6251-MONOMER
ECOLIWIKI:
b0454
INTERPRO:
IPR014048
INTERPRO:
IPR036388
INTERPRO:
IPR036217
MODBASE:
P0AFP2
PFAM:
PF01035
PRIDE:
P0AFP2
REFSEQ:
NP_414988
SMR:
P0AFP2
UNIPROT:
P0AFP2


Operon      
Name: ybaZ         
Operon arrangement:
Transcription unit        Promoter
ybaZ


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 ffsp6 476288 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ffsp5 476399 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ffsp7 476422 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_610 476448 forward nd [RS-EPT-CBR] [6]


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] Chen CS., Korobkova E., Chen H., Zhu J., Jian X., Tao SC., He C., Zhu H., 2008, A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli., Nat Methods 5(1):69-74

 [2] Mazon G., Philippin G., Cadet J., Gasparutto D., Fuchs RP., 2009, The alkyltransferase-like ybaZ gene product enhances nucleotide excision repair of O(6)-alkylguanine adducts in E. coli., DNA Repair (Amst) 8(6):697-703

 [3] Mazon G., Philippin G., Cadet J., Gasparutto D., Modesti M., Fuchs RP., 2010, Alkyltransferase-like protein (eATL) prevents mismatch repair-mediated toxicity induced by O6-alkylguanine adducts in Escherichia coli., Proc Natl Acad Sci U S A 107(42):18050-5

 [4] Tomaszowski KH., Aasland D., Margison GP., Williams E., Pinder SI., Modesti M., Fuchs RP., Kaina B., 2015, The bacterial alkyltransferase-like (eATL) protein protects mammalian cells against methylating agent-induced toxicity., DNA Repair (Amst) 28:14-20

 [5] 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

 [6] 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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