RegulonDB RegulonDB 10.7: Gene Form
   

pdeR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdeR yciZ ymiD ymiB FliZ pdeRp pdeRp TSS_1731 TSS_1731 yciZp yciZp TSS_1730 TSS_1730 yciTp1 yciTp1 yciTp yciTp

Gene      
Name: pdeR    Texpresso search in the literature
Synonym(s): ECK1280, G6639, b1285, gmr, yciR
Genome position(nucleotides): 1344757 <-- 1346742 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.49
External database links:  
ASAP:
ABE-0004317
ECHOBASE:
EB3191
OU-MICROARRAY:
b1285
PORTECO:
gmr
REGULONDB:
b1285
STRING:
511145.b1285
M3D: pdeR
COLOMBOS: pdeR
PortEco: b1285


Product      
Name: cyclic di-GMP phosphodiesterase PdeR
Synonym(s): Gmr, PdeR, YciR
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 74.665
Isoelectric point: 6.722
Motif(s):
 
Type Positions Sequence
175 -> 175 V
256 -> 256 D
123 -> 225 AIVILDSRGNIQRFNRLCEDYTGLKEHDVIGQSVFKLFMSRREAAASRRNNRVFFRSGNAYEVELWIPTCKGQRLFLFRNKFVHSGSGKNEIFLICSGTDITE
344 -> 344 P
412 -> 644 NLRKALENDQLVIHYQPKITWRGEVRSLEALVRWQSPERGLIPPLDFISYAEESGLIVPLGRWVILDVVRQVAKWRDKGINLRVAVNISARQLADQTIFTALKQVLQELNFEYCPIDVELTESCLIENDELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQVFVRDIHKQPVSQSLVRAIVAVAQALNLQVIAEGVESAKEDAFLTKNGINERQGFLFAKP

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  5 - cell processes --> 5.5 - adaptations
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0005525 - GTP binding
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity
biological_process GO:0010608 - posttranscriptional regulation of gene expression
GO:0019935 - cyclic-nucleotide-mediated signaling
GO:0031280 - negative regulation of cyclase activity
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Cairrao F., et al., 2001
[2] Cimdins A., et al., 2017
[3] Somorin YM., et al., 2018
External database links:  
DIP:
DIP-11590N
ECOCYC:
G6639-MONOMER
ECOLIWIKI:
b1285
INTERPRO:
IPR000014
INTERPRO:
IPR035965
INTERPRO:
IPR000160
INTERPRO:
IPR001633
INTERPRO:
IPR029787
INTERPRO:
IPR035919
MINT:
P77334
MODBASE:
P77334
PFAM:
PF13426
PFAM:
PF00990
PFAM:
PF00563
PRIDE:
P77334
PRODB:
PRO_000022822
PROSITE:
PS50887
PROSITE:
PS50883
PROSITE:
PS50112
PROTEINMODELPORTAL:
P77334
REFSEQ:
NP_415801
SMART:
SM00052
SMART:
SM00091
SMART:
SM00267
SMR:
P77334
UNIPROT:
P77334


Operon      
Name: pdeR         
Operon arrangement:
Transcription unit        Promoter
pdeR


Transcriptional Regulation      
Display Regulation             
Repressed by: FliZ, RutR


RNA cis-regulatory element    
Attenuation: Transcriptional


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 yciTp1 1344544 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1730 1344637 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_1731 1346842 reverse nd [RS-EPT-CBR] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Cairrao F., Chora A., Zilhao R., Carpousis AJ., Arraiano CM., 2001, RNase II levels change according to the growth conditions: characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II., Mol Microbiol 39(6):1550-61

 [2] Cimdins A., Simm R., Li F., Luthje P., Thorell K., Sjoling Å., Brauner A., Romling U., 2017, Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli., Microbiologyopen 6(5)

 [3] Somorin YM., Vollmerhausen T., Waters N., Pritchard L., Abram F., Brennan F., O'Byrne C., 2018, Absence of Curli in Soil-Persistent Escherichia coli Is Mediated by a C-di-GMP Signaling Defect and Suggests Evidence of Biofilm-Independent Niche Specialization., Front Microbiol 9:1340

 [4] 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

 [5] 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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