RegulonDB RegulonDB 11.1: Gene Form
   

nudC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hemE nudC rsd TSS_4822 TSS_4822 TSS_4821 (cluster) TSS_4821 (cluster) TSS_4820 TSS_4820 rsdp1 rsdp1 rsdp2 rsdp2 nudCp2 nudCp2 nudCp5 nudCp5 TSS_4819 TSS_4819 TSS_4818 (cluster) TSS_4818 (cluster)

Gene      
Name: nudC    Texpresso search in the literature
Synonym(s): ECK3988, EG11702, b3996, yjaD
Genome position(nucleotides): 4196903 --> 4197676
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.23
External database links:  
ASAP:
 ABE-0013063
ECHOBASE:
 EB1653
ECOLIHUB:
 nudC
OU-MICROARRAY:
 b3996
STRING:
 511145.b3996
COLOMBOS: nudC


Product      
Name: RNA decapping hydrolase
Synonym(s): NADH pyrophosphatase, NudC, YjaD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 29.689
Isoelectric point: 5.588
Motif(s):
 
Type Positions Sequence Comment
33 -> 33 A UniProt: In Ref. 2; AAC43094..
69 -> 69 R UniProt: Does not affect deNADding activity..
93 -> 124 RSHKYCGYCGHEMYPSKTEWAMLCSHCRERYY
125 -> 248 PQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDT UniProt: Nudix hydrolase.
132 -> 234 IVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLL

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.2 - nucleotides
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0110153 - RNA NAD-cap (NMN-forming) hydrolase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0000210 - NAD+ diphosphatase activity
GO:0000287 - magnesium ion binding
GO:0030145 - manganese ion binding
GO:0042803 - protein homodimerization activity
GO:0035529 - NADH pyrophosphatase activity
biological_process GO:0006734 - NADH metabolic process
GO:0019677 - NAD catabolic process
GO:0006742 - NADP catabolic process
GO:0110155 - NAD-cap decapping
GO:0006402 - mRNA catabolic process
GO:0048255 - mRNA stabilization
GO:0034661 - ncRNA catabolic process
External database links:  
ALPHAFOLD:
 P32664
ECOCYC:
 EG11702-MONOMER
ECOLIWIKI:
 b3996
INTERPRO:
 IPR000086
INTERPRO:
 IPR022925
INTERPRO:
 IPR020084
INTERPRO:
 IPR015797
INTERPRO:
 IPR015376
MODBASE:
 P32664
PDB:
 5IW5
PDB:
 5IW4
PDB:
 5ISY
PDB:
 1VK6
PDB:
 2GB5
PFAM:
 PF00293
PFAM:
 PF09297
PRIDE:
 P32664
PRODB:
 PRO_000023421
PROSITE:
 PS51462
PROSITE:
 PS00893
REFSEQ:
 YP_026280
SMR:
 P32664
UNIPROT:
 P32664


Operon      
Name: nudC-hemE-nfi         
Operon arrangement:
Transcription unit        Promoter
nudC-hemE-nfi


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_4818 (cluster) 4196683 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4819 4196698 forward nd [RS-EPT-CBR] [1]
  promoter nudCp5 4196714 forward nd [COMP-AINF] [2]
  promoter nudCp2 4196719 forward nd [COMP-AINF] [2]
  promoter TSS_4820 4197692 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4821 (cluster) 4198655 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4822 4198700 forward 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