RegulonDB RegulonDB 11.1: Gene Form
   

ribD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ribD ribE nrdR TSS_535 TSS_535 TSS_534 TSS_534 TSS_533 TSS_533 TSS_532 TSS_532 TSS_531 (cluster) TSS_531 (cluster) TSS_530 (cluster) TSS_530 (cluster) ribEp ribEp TSS_528 TSS_528 yajIp6 yajIp6

Gene      
Name: ribD    Texpresso search in the literature
Synonym(s): ECK0408, EG11321, b0414, nusII, ribG, ybaE
Genome position(nucleotides): 433455 --> 434558
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.34
External database links:  
ASAP:
 ABE-0001441
CGSC:
 35685
ECHOBASE:
 EB1297
ECOLIHUB:
 ribD
OU-MICROARRAY:
 b0414
STRING:
 511145.b0414
COLOMBOS: ribD


Product      
Name: fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase
Synonym(s): RibD, RibG, YbaE
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 40.338
Isoelectric point: 7.644
Motif(s):
 
Type Positions Sequence Comment
1 -> 123 MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGIDVS UniProt: CMP/dCMP-type deaminase.
2 -> 99 QDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVAS
146 -> 367 FPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCLHLVGA UniProt: Reductase; Sequence Annotation Type: region of interest.
147 -> 362 PYIQLKLGASLDGRTAMASGESQWITSPQARRDVQLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTPVHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEAGPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDVCL
161 -> 164 TAMA UniProt: NADP.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.9 - riboflavin
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008703 - 5-amino-6-(5-phosphoribosylamino)uracil reductase activity
GO:0008835 - diaminohydroxyphosphoribosylaminopyrimidine deaminase activity
GO:0008270 - zinc ion binding
GO:0050661 - NADP binding
biological_process GO:0008152 - metabolic process
GO:0009231 - riboflavin biosynthetic process
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P25539
DIP:
 DIP-10708N
ECOCYC:
 RIBOFLAVINSYNDEAM-MONOMER
ECOLIWIKI:
 b0414
INTERPRO:
 IPR016193
INTERPRO:
 IPR024072
INTERPRO:
 IPR016192
INTERPRO:
 IPR011549
INTERPRO:
 IPR004794
INTERPRO:
 IPR002734
INTERPRO:
 IPR002125
MODBASE:
 P25539
PDB:
 2G6V
PDB:
 2O7P
PDB:
 2OBC
PFAM:
 PF01872
PFAM:
 PF00383
PRIDE:
 P25539
PRODB:
 PRO_000023752
PROSITE:
 PS00903
PROSITE:
 PS51747
REFSEQ:
 NP_414948
SMR:
 P25539
UNIPROT:
 P25539


Operon      
Name: nrdR-ribDE-nusB-thiL-pgpA         
Operon arrangement:
Transcription unit        Promoter
nrdR-ribDE-nusB-thiL-pgpA
ribE-nusB-thiL-pgpA


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 yajIp6 433034 reverse nd [COMP-AINF] [1]
  promoter TSS_528 434501 forward nd [RS-EPT-CBR] [2]
  promoter TSS_530 (cluster) 434511 forward nd [RS-EPT-CBR] [2]
  promoter TSS_531 (cluster) 434593 forward nd [RS-EPT-CBR] [2]
  promoter TSS_532 434596 forward nd [RS-EPT-CBR] [2]
  promoter TSS_533 434599 forward nd [RS-EPT-CBR] [2]
  promoter TSS_534 434604 forward nd [RS-EPT-CBR] [2]
  promoter TSS_535 434974 forward nd [RS-EPT-CBR] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] 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

 [2] 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.

RegulonDB