RegulonDB RegulonDB 11.1: Gene Form
   

yhbO gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yraR yhbO yhbP yhbQ yhbS terminator anti-terminator anti-anti-terminator anti-anti-terminator anti-terminator terminator yhbQp2 yhbQp2 TSS_3420 TSS_3420 yraRp1 yraRp1 yraRp6 yraRp6 TSS_3419 TSS_3419 yraRp yraRp

Gene      
Name: yhbO    Texpresso search in the literature
Synonym(s): ECK3141, G7647, b3153
Genome position(nucleotides): 3298974 --> 3299492
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.29
External database links:  
ASAP:
 ABE-0010361
ECHOBASE:
 EB2637
ECOLIHUB:
 yhbO
OU-MICROARRAY:
 b3153
STRING:
 511145.b3153
COLOMBOS: yhbO


Product      
Name: protein/nucleic acid deglycase 2
Synonym(s): Maillard deglycase 2, YhbO
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.858
Isoelectric point: 5.092
Motif(s):
 
Type Positions Sequence Comment
2 -> 172 SKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA UniProt: Protein/nucleic acid deglycase 2.
3 -> 167 KKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREAL
104 -> 104 C UniProt: Unable to complement the gene deletion mutant, in contrast to the wild-type allele that rescues the oxidative-stress and thermal-stress sensitive phenotypes..

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016787 - hydrolase activity
GO:0042802 - identical protein binding
GO:0019172 - glyoxalase III activity
GO:0036524 - protein deglycase activity
biological_process GO:0106044 - guanine deglycation
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006979 - response to oxidative stress
GO:0009408 - response to heat
GO:0030091 - protein repair
GO:0009268 - response to pH
GO:0009411 - response to UV
GO:0019249 - lactate biosynthetic process
GO:0061727 - methylglyoxal catabolic process to lactate
GO:0036525 - protein deglycation
Note(s): Note(s): ...[more].
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Abdallah J., et al., 2007
[2] McCloskey D., et al., 2018
[3] Weber H., et al., 2005
External database links:  
ALPHAFOLD:
 P45470
DIP:
 DIP-12263N
ECOCYC:
 G7647-MONOMER
ECOLIWIKI:
 b3153
INTERPRO:
 IPR006286
INTERPRO:
 IPR002818
INTERPRO:
 IPR029062
MODBASE:
 P45470
PDB:
 1OI4
PFAM:
 PF01965
PRIDE:
 P45470
PROSITE:
 PS51276
REFSEQ:
 NP_417622
SMR:
 P45470
SWISSMODEL:
 P45470
UNIPROT:
 P45470


Operon      
Name: yhbO         
Operon arrangement:
Transcription unit        Promoter
yhbO


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_3419 3298912 reverse nd [RS-EPT-CBR] [4]
  promoter yraRp6 3298923 reverse nd [COMP-AINF] [5]
  promoter yraRp1 3299012 reverse nd [COMP-AINF] [5]
  promoter TSS_3420 3299936 reverse nd [RS-EPT-CBR] [4]
  promoter yhbQp2 3299939 forward nd [COMP-AINF] [5]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Abdallah J., Caldas T., Kthiri F., Kern R., Richarme G., 2007, YhbO protects cells against multiple stresses., J Bacteriol 189(24):9140-4

 [2] McCloskey D., Xu S., Sandberg TE., Brunk E., Hefner Y., Szubin R., Feist AM., Palsson BO., 2018, Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes., Metab Eng 48:82-93

 [3] Weber H., Polen T., Heuveling J., Wendisch VF., Hengge R., 2005, Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity., J Bacteriol 187(5):1591-603

 [4] 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.

 [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

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