RegulonDB RegulonDB 10.9: Gene Form
   

ybaK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ushA ybaK chiX ybaP TSS_648 TSS_648 TSS_647 TSS_647 TSS_646 TSS_646 chiXp chiXp

Gene      
Name: ybaK    Texpresso search in the literature
Synonym(s): ECK0475, EG12454, b0481
Genome position(nucleotides): 506603 <-- 507082 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.83
External database links:  
ASAP:
ABE-0001670
ECHOBASE:
EB2348
ECOLIHUB:
ybaK
OU-MICROARRAY:
b0481
STRING:
511145.b0481
COLOMBOS: ybaK


Product      
Name: Cys-tRNAPro and Cys-tRNACys deacylase
Synonym(s): YbaK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.093
Isoelectric point: 9.633
Motif(s):
 
Type Positions Sequence
136 -> 136 D
30 -> 30 G
31 -> 146 DEVVKKLGLNPDQVYKTLLVAVNGDMKHLAVAVTPVAGQLDLKKVAKALGAKKVEMADPMVAQRSTGYLVGGISPLGQKKRLPTIIDAPAQEFATIYVSGGKRGLDIELAAGDLAK

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.1 - amino acid -activation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016829 - lyase activity
GO:0002161 - aminoacyl-tRNA editing activity
GO:0043907 - Cys-tRNA(Pro) hydrolase activity
biological_process GO:0106074 - aminoacyl-tRNA metabolism involved in translational fidelity
GO:0010165 - response to X-ray
GO:0006412 - translation
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IE] Inferred from experiment
Reference(s): [1] Kumar S., et al., 2013
[2] Liu Z., et al., 2015
[3] Ruan B., et al., 2005
[4] Vargas-Rodriguez O., et al., 2013
External database links:  
DIP:
DIP-48133N
ECOCYC:
EG12454-MONOMER
ECOLIWIKI:
b0481
INTERPRO:
IPR036754
INTERPRO:
IPR007214
INTERPRO:
IPR004369
MODBASE:
P0AAR3
PDB:
2DXA
PFAM:
PF04073
PRIDE:
P0AAR3
REFSEQ:
NP_415014
SMR:
P0AAR3
SWISSMODEL:
P0AAR3
UNIPROT:
P0AAR3


Operon      
Name: ybaK         
Operon arrangement:
Transcription unit        Promoter
ybaK


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_646 507216 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_647 507236 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_648 507241 reverse nd [RS-EPT-CBR] [5]


Evidence    

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



Reference(s)    

 [1] Kumar S., Das M., Hadad CM., Musier-Forsyth K., 2013, Aminoacyl-tRNA substrate and enzyme backbone atoms contribute to translational quality control by YbaK., J Phys Chem B 117(16):4521-7

 [2] Liu Z., Vargas-Rodriguez O., Goto Y., Novoa EM., Ribas de Pouplana L., Suga H., Musier-Forsyth K., 2015, Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation., Proc Natl Acad Sci U S A 112(19):6027-32

 [3] Ruan B., Soll D., 2005, The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase., J Biol Chem 280(27):25887-91

 [4] Vargas-Rodriguez O., Musier-Forsyth K., 2013, Exclusive use of trans-editing domains prevents proline mistranslation., J Biol Chem 288(20):14391-9

 [5] 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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