RegulonDB RegulonDB 11.1: Gene Form
   

ymdB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

clsC ymdB ymdA terminator clsCp clsCp ymdBp ymdBp TSS_1326 TSS_1326 ymdBp4 ymdBp4 ymdBp3 ymdBp3

Gene      
Name: ymdB    Texpresso search in the literature
Synonym(s): ECK1031, G6550, b1045
Genome position(nucleotides): 1105820 --> 1106353
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.69
External database links:  
ASAP:
 ABE-0003549
ECHOBASE:
 EB3633
ECOLIHUB:
 ymdB
OU-MICROARRAY:
 b1045
STRING:
 511145.b1045
COLOMBOS: ymdB


Product      
Name: 2'-O-acetyl-ADP-ribose deacetylase, regulator of RNase III activity
Synonym(s): YmdB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.88
Isoelectric point: 5.525
Motif(s):
 
Type Positions Sequence Comment
1 -> 175 MKTRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQQG UniProt: Macro.
11 -> 12 DI UniProt: Substrate binding; Sequence Annotation Type: region of interest.
21 -> 137 VNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIA
25 -> 25 N UniProt: 5-fold decrease in catalytic efficiency. Loss of activity; when associated with A-35..
33 -> 35 GVD UniProt: Substrate binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016787 - hydrolase activity
GO:0008428 - ribonuclease inhibitor activity
GO:0019899 - enzyme binding
GO:0019213 - deacetylase activity
GO:0001883 - purine nucleoside binding
GO:0060698 - endoribonuclease inhibitor activity
GO:0061463 - O-acetyl-ADP-ribose deacetylase activity
biological_process GO:0042278 - purine nucleoside metabolic process
GO:0046677 - response to antibiotic
GO:0060701 - negative regulation of ribonuclease activity
GO:0060702 - negative regulation of endoribonuclease activity
GO:1900231 - regulation of single-species biofilm formation on inanimate substrate
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0A8D6
DIP:
 DIP-48222N
ECOCYC:
 G6550-MONOMER
ECOLIWIKI:
 b1045
INTERPRO:
 IPR024900
INTERPRO:
 IPR002589
INTERPRO:
 IPR043472
MODBASE:
 P0A8D6
PDB:
 1SPV
PDB:
 5CMS
PDB:
 5CB3
PDB:
 5CB5
PFAM:
 PF01661
PRIDE:
 P0A8D6
PROSITE:
 PS51154
REFSEQ:
 NP_415563
SMART:
 SM00506
SMR:
 P0A8D6
UNIPROT:
 P0A8D6


Operon      
Name: ymdAB-clsC         
Operon arrangement:
Transcription unit        Promoter
ymdA
ymdAB
ymdAB-clsC
ymdB
ymdB-clsC
clsC


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 ymdBp3 1105714 forward nd [COMP-AINF] [1]
  promoter ymdBp4 1105738 forward nd [COMP-AINF] [1]
  promoter TSS_1326 1105797 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.

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