RegulonDB RegulonDB 11.1: Gene Form
   

ycaO gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycaO focA ycaP FNR NarL NarL NarL NarL NarL ArcA NarL NarL NarL ArcA IHF NarL FNR NarL CRP NarL ArcA anti-terminator terminator terminator focAp3 focAp3 focAp2 focAp2 focAp1 focAp1 TSS_1168 TSS_1168 TSS_1167 (cluster) TSS_1167 (cluster) TSS_1166 (cluster) TSS_1166 (cluster) TSS_1165 TSS_1165 TSS_1164 TSS_1164 TSS_1163 TSS_1163 TSS_1162 TSS_1162 TSS_1161 TSS_1161 pflBp5 pflBp5 TSS_1160 TSS_1160 TSS_1159 TSS_1159 pflBp4 pflBp4 TSS_1158 (cluster) TSS_1158 (cluster) TSS_1157 TSS_1157 TSS_1156 (cluster) TSS_1156 (cluster) pflBp3 pflBp3 TSS_1155 TSS_1155 TSS_1154 TSS_1154 pflBp2 pflBp2

Gene      
Name: ycaO    Texpresso search in the literature
Synonym(s): ECK0896, G6468, b0905
Genome position(nucleotides): 954872 <-- 956632
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.56
External database links:  
ASAP:
 ABE-0003081
ECHOBASE:
 EB3463
ECOLIHUB:
 ycaO
OU-MICROARRAY:
 b0905
STRING:
 511145.b0905
COLOMBOS: ycaO


Product      
Name: ribosomal protein S12 methylthiotransferase accessory factor YcaO
Synonym(s): YcaO, protein involved in beta;-methylthiolation of ribosomal protein S12
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 65.652
Isoelectric point: 4.113
Motif(s):
 
Type Positions Sequence Comment
59 -> 391 NGKGATKKAALASALGEYFERLSTNYFFADFWLGETIANGPFVHYPNEKWFPLTENDDVPEGLLDDRLRAFYDPENELTGSMLIDLQSGNEDRGICGLPFTRQSDNQTVYIPMNIIGNLYVSNGMSAGNTRNEARVQGLSEVFERYVKNRIIAESISLPEIPADVLARYPAVVEAIETLEAEGFPIFAYDGSLGGQYPVICVVLFNPANGTCFASFGAHPDFGVALERTVTELLQGRGLKDLDVFTPPTFDDEEVAEHTNLETHFIDSSGLISWDLFKQDADYPFVDWNFSGTTEEEFATLMAIFNKEDKEVYIADYEHLGVYACRIIVPGMS
60 -> 437 GKGATKKAALASALGEYFERLSTNYFFADFWLGETIANGPFVHYPNEKWFPLTENDDVPEGLLDDRLRAFYDPENELTGSMLIDLQSGNEDRGICGLPFTRQSDNQTVYIPMNIIGNLYVSNGMSAGNTRNEARVQGLSEVFERYVKNRIIAESISLPEIPADVLARYPAVVEAIETLEAEGFPIFAYDGSLGGQYPVICVVLFNPANGTCFASFGAHPDFGVALERTVTELLQGRGLKDLDVFTPPTFDDEEVAEHTNLETHFIDSSGLISWDLFKQDADYPFVDWNFSGTTEEEFATLMAIFNKEDKEVYIADYEHLGVYACRIIVPGMSDIYPAEDLWLANNSMGSHLRETILSLPGSEWEKEDYLNLIEQLDEE UniProt: YcaO.
71 -> 79 SALGEYFER ATP binding motif; conserved in members of the YcaO superfamily
184 -> 203 SAGNTRNEARVQGLSEVFER ATP binding motif; conserved in members of the YcaO superfamily
286 -> 290 RTVTE ATP binding motif; conserved in members of the YcaO superfamily

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0000287 - magnesium ion binding
GO:0047693 - ATP diphosphatase activity
biological_process GO:0018339 - peptidyl-L-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Strader MB., et al., 2011
[2] Tenorio E., et al., 2003
External database links:  
ALPHAFOLD:
 P75838
DIP:
 DIP-11470N
ECOCYC:
 G6468-MONOMER
ECOLIWIKI:
 b0905
INTERPRO:
 IPR003776
INTERPRO:
 IPR041080
PDB:
 4Q86
PDB:
 4Q84
PDB:
 4Q85
PFAM:
 PF02624
PFAM:
 PF18381
PRIDE:
 P75838
PROSITE:
 PS51664
REFSEQ:
 NP_415425
SMR:
 P75838
UNIPROT:
 P75838


Operon      
Name: ycaO         
Operon arrangement:
Transcription unit        Promoter
ycaO


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_1154 953645 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1155 953648 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1156 (cluster) 953745 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1157 953777 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1158 (cluster) 953824 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1159 953919 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1160 953922 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1161 954185 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1162 954226 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1163 954310 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1164 954317 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1165 954328 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1166 (cluster) 954442 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1167 (cluster) 954449 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1168 954492 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Strader MB., Costantino N., Elkins CA., Chen CY., Patel I., Makusky AJ., Choy JS., Court DL., Markey SP., Kowalak JA., 2011, A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12., Mol Cell Proteomics 10(3):M110.005199

 [2] Tenorio E., Saeki T., Fujita K., Kitakawa M., Baba T., Mori H., Isono K., 2003, Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation., FEMS Microbiol Lett 225(1):107-14

 [3] 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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