RegulonDB RegulonDB 10.6.3: Gene Form
   

deoD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yjjJ deoB deoD terminator anti-terminator anti-anti-terminator terminator anti-terminator anti-anti-terminator yjjJp4 yjjJp4 yjjJp2 yjjJp2 TSS_5171 TSS_5171 TSS_5170 TSS_5170 TSS_5169 TSS_5169 TSS_5168 TSS_5168 TSS_5167 TSS_5167

Gene      
Name: deoD    Texpresso search in the literature
Synonym(s): ECK4376, EG10222, b4384, pup
Genome position(nucleotides): 4620883 --> 4621602 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.36
External database links:  
ASAP:
ABE-0014379
CGSC:
865
ECHOBASE:
EB0218
ECOCYC:
EG10222
ECOLIHUB:
deoD
NCBI-GENE:
945654
OU-MICROARRAY:
b4384
REGULONDB:
b4384
STRING:
511145.b4384
M3D: deoD
COLOMBOS: deoD
PortEco: b4384


Product      
Name: purine nucleoside phosphorylase
Synonym(s): DeoD, Pup
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 25.95
Isoelectric point: 5.359
Motif(s):
 
Type Positions Sequence
204 -> 205 SD
2 -> 239 ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDKE
15 -> 218 DVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAER
88 -> 91 RVGS
180 -> 182 EME

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016757 - transferase activity, transferring glycosyl groups
GO:0016740 - transferase activity
GO:0004731 - purine-nucleoside phosphorylase activity
GO:0016763 - transferase activity, transferring pentosyl groups
GO:0042802 - identical protein binding
biological_process GO:0006139 - nucleobase-containing compound metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0009116 - nucleoside metabolic process
GO:0006152 - purine nucleoside catabolic process
GO:0042278 - purine nucleoside metabolic process
GO:0019686 - purine nucleoside interconversion
External database links:  
DIP:
DIP-36195N
ECOCYC:
DEOD-MONOMER
ECOLIWIKI:
b4384
INTERPRO:
IPR018016
INTERPRO:
IPR000845
INTERPRO:
IPR004402
INTERPRO:
IPR035994
MINT:
P0ABP8
MODBASE:
P0ABP8
PANTHER:
PTHR43691:SF2
PDB:
1OTX
PDB:
5IU6
PDB:
5I3C
PDB:
4TTJ
PDB:
4TTI
PDB:
4TTA
PDB:
4TS9
PDB:
4TS3
PDB:
1A69
PDB:
1ECP
PDB:
1K9S
PDB:
1OTY
PDB:
1OU4
PDB:
1OUM
PDB:
1OV6
PDB:
1OVG
PDB:
3ONV
PDB:
3OOE
PDB:
3OOH
PDB:
3OPV
PDB:
3UT6
PFAM:
PF01048
PRIDE:
P0ABP8
PRODB:
PRO_000022430
PROSITE:
PS01232
PROTEINMODELPORTAL:
P0ABP8
REFSEQ:
NP_418801
SMR:
P0ABP8
UNIPROT:
P0ABP8


Operon      
Name: deoCABD         
Operon arrangement:
Transcription unit        Promoter
deoCABD
deoCABD
deoBD
deoA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Fis
Repressed by: CRP, DeoR, ModE, CytR


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 TSS_5167 4619991 forward nd [RS-EPT-CBR] [1]
  promoter TSS_5168 4620783 forward nd [RS-EPT-CBR] [1]
  promoter TSS_5169 4620785 forward nd [RS-EPT-CBR] [1]
  promoter TSS_5170 4620789 forward nd [RS-EPT-CBR] [1]
  promoter TSS_5171 4621110 forward nd [RS-EPT-CBR] [1]
  promoter yjjJp2 4621657 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yjjJp4 4621716 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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


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