RegulonDB RegulonDB 10.8: Gene Form
   

holE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yobB yobA holE FnrS TSS_2187 (cluster) TSS_2187 (cluster) TSS_2186 TSS_2186 yobBp5 yobBp5 TSS_2185 TSS_2185 yobBp8 yobBp8 TSS_2184 TSS_2184 holEp6 holEp6 holEp4 holEp4 holEp5 holEp5

Gene      
Name: holE    Texpresso search in the literature
Synonym(s): ECK1843, EG11505, b1842
Genome position(nucleotides): 1925108 --> 1925338 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.48
External database links:  
ASAP:
ABE-0006126
CGSC:
31439
ECHOBASE:
EB1468
OU-MICROARRAY:
b1842
PortEco:
holE
STRING:
511145.b1842
COLOMBOS: holE


Product      
Name: DNA polymerase III subunit θ
Synonym(s): HolE
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 8.846
Isoelectric point: 9.721
Motif(s):
 
Type Positions Sequence
4 -> 71 NLAKLDQTEMDKVNVDLAAAGVAFKERYNMPVIAEAVEREQPEHLRSWFRERLIAHRLASVNLSRLPY

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0044776 - DNA polymerase III, core complex
molecular_function GO:0003677 - DNA binding
GO:0003887 - DNA-directed DNA polymerase activity
GO:0016779 - nucleotidyltransferase activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
biological_process GO:0006260 - DNA replication
GO:0071897 - DNA biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] DeRose EF., et al., 2003
[2] Gupta R., et al., 2004
[3] Jonczyk P., et al., 1998
[4] Kim DR., et al., 1996
[5] Li D., et al., 1999
[6] Ozawa K., et al., 2013
[7] Ozawa K., et al., 2008
External database links:  
DIP:
DIP-39982N
ECOCYC:
EG11505-MONOMER
ECOLIWIKI:
b1842
INTERPRO:
IPR036745
INTERPRO:
IPR009052
MINT:
P0ABS8
MODBASE:
P0ABS8
PDB:
1DU2
PDB:
2AE9
PDB:
5M1S
PDB:
2AXD
PDB:
2XY8
PFAM:
PF06440
PRIDE:
P0ABS8
PRODB:
PRO_000022920
PRODOM:
PD057609
REFSEQ:
NP_416356
SMR:
P0ABS8
UNIPROT:
P0ABS8


Operon      
Name: holE         
Operon arrangement:
Transcription unit        Promoter
 


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 holEp5 1925020 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter holEp4 1925029 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter holEp6 1925086 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2184 1925088 forward nd [RS-EPT-CBR] [9]
  promoter yobBp8 1925209 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2185 1925307 reverse nd [RS-EPT-CBR] [9]
  promoter yobBp5 1925364 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2186 1925389 forward nd [RS-EPT-CBR] [9]
  promoter TSS_2187 (cluster) 1926096 forward For this promoter, there
Read more >
[RS-EPT-CBR] [9]


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] DeRose EF., Darden T., Harvey S., Gabel S., Perrino FW., Schaaper RM., London RE., 2003, Elucidation of the epsilon-theta subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy., Biochemistry 42(13):3635-44

 [2] Gupta R., Hamdan SM., Dixon NE., Sheil MM., Beck JL., 2004, Application of electrospray ionization mass spectrometry to study the hydrophobic interaction between the epsilon and theta subunits of DNA polymerase III., Protein Sci 13(11):2878-87

 [3] Jonczyk P., Nowicka A., Fijalkowska IJ., Schaaper RM., Ciesla Z., 1998, In vivo protein interactions within the Escherichia coli DNA polymerase III core., J Bacteriol 180(6):1563-6

 [4] Kim DR., McHenry CS., 1996, In vivo assembly of overproduced DNA polymerase III. Overproduction, purification, and characterization of the alpha, alpha-epsilon, and alpha-epsilon-theta subunits., J Biol Chem 271(34):20681-9

 [5] Li D., Allen DL., Harvey S., Perrino FW., Schaaper RM., London RE., 1999, A preliminary CD and NMR study of the Escherichia coli DNA polymerase III theta subunit., Proteins 36(1):111-6

 [6] Ozawa K., Horan NP., Robinson A., Yagi H., Hill FR., Jergic S., Xu ZQ., Loscha KV., Li N., Tehei M., Oakley AJ., Otting G., Huber T., Dixon NE., 2013, Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain., Nucleic Acids Res 41(10):5354-67

 [7] Ozawa K., Jergic S., Park AY., Dixon NE., Otting G., 2008, The proofreading exonuclease subunit epsilon of Escherichia coli DNA polymerase III is tethered to the polymerase subunit alpha via a flexible linker., Nucleic Acids Res 36(15):5074-82

 [8] 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

 [9] 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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