RegulonDB RegulonDB 11.1: Gene Form
   

roxA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

phoQ pepT roxA terminator TSS_1469 TSS_1469 TSS_1468 TSS_1468 ycfDp5 ycfDp5 ycfDp4 ycfDp4 TSS_1466 (cluster) TSS_1466 (cluster)

Gene      
Name: roxA    Texpresso search in the literature
Synonym(s): ECK1114, EG11430, b1128, ycfD
Genome position(nucleotides): 1187119 <-- 1188240
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.01
External database links:  
ASAP:
 ABE-0003802
ECHOBASE:
 EB1400
ECOLIHUB:
 ycfD
OU-MICROARRAY:
 b1128
STRING:
 511145.b1128
COLOMBOS: roxA


Product      
Name: 50S ribosomal protein L16-arginine 3-hydroxylase
Synonym(s): RoxA, YcfD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 42.579
Isoelectric point: 4.444
Motif(s):
 
Type Positions Sequence Comment
92 -> 219 PTAALMRPFRELPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEKLQMKQHCPHPDLLQVDPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNTRELISGFADYVL UniProt: JmjC.
96 -> 210 LMRPFRELPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEKLQMKQHCPHPDLLQVDPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNTREL
116 -> 116 S UniProt: Loss of binding of 2-oxoglutarate..
125 -> 127 HLD UniProt: Substrate-binding; Sequence Annotation Type: region of interest.
140 -> 140 R UniProt: Loss of binding of 2-oxoglutarate..

 
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:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0016706 - 2-oxoglutarate-dependent dioxygenase activity
GO:0008198 - ferrous iron binding
GO:0051213 - dioxygenase activity
GO:0042803 - protein homodimerization activity
biological_process GO:0043687 - post-translational protein modification
GO:0030961 - peptidyl-arginine hydroxylation
External database links:  
ALPHAFOLD:
 P27431
DIP:
 DIP-11535N
ECOCYC:
 EG11430-MONOMER
ECOLIWIKI:
 b1128
INTERPRO:
 IPR039994
INTERPRO:
 IPR003347
MODBASE:
 P27431
PANTHER:
 PTHR13096
PDB:
 4NUB
PDB:
 4LIV
PDB:
 4LIU
PDB:
 4LIT
PDB:
 4CCL
PFAM:
 PF08007
PFAM:
 PF20514
PRIDE:
 P27431
PROSITE:
 PS51184
REFSEQ:
 NP_415646
SMART:
 SM00558
SMR:
 P27431
UNIPROT:
 P27431


Operon      
Name: roxA         
Operon arrangement:
Transcription unit        Promoter
roxA


RNA cis-regulatory element    
Attenuation: Translational


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_1466 (cluster) 1188265 reverse nd [RS-EPT-CBR] [1]
  promoter ycfDp4 1188267 reverse nd [COMP-AINF], [RS-EPT-CBR] [1], [2]
  promoter ycfDp5 1188270 reverse nd [COMP-AINF] [2]
  promoter TSS_1468 1189078 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1469 1189096 reverse nd [RS-EPT-CBR] [1]


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] 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.

 [2] 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

RegulonDB