RegulonDB RegulonDB 10.9: Gene Form
   

hpf gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpoN ptsN hpf terminator TSS_3525 TSS_3525 TSS_3524 TSS_3524 TSS_3523 TSS_3523 TSS_3522 TSS_3522 TSS_3521 TSS_3521 TSS_3520 TSS_3520 TSS_3519 TSS_3519 TSS_3518 TSS_3518 TSS_3517 TSS_3517 TSS_3516 TSS_3516 TSS_3515 TSS_3515 TSS_3514 (cluster) TSS_3514 (cluster)

Gene      
Name: hpf    Texpresso search in the literature
Synonym(s): ECK3192, EG11681, b3203, yhbH
Genome position(nucleotides): 3346173 --> 3346460 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.79
External database links:  
ASAP:
ABE-0010516
ECHOBASE:
EB1632
ECOLIHUB:
hpf
OU-MICROARRAY:
b3203
STRING:
511145.b3203
COLOMBOS: hpf


Shine dalgarno      
Sequence: ccaaccgataAGGAAGacactATG


Product      
Name: ribosome hibernation-promoting factor
Synonym(s): Hpf, YhbH
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 10.75
Isoelectric point: 7.088
Motif(s):
 
Type Positions Sequence
3 -> 93 LNITGNNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHTSDATLHVNGGEIHASAEGQDMYAAIDGLIDKLARQLTKHKDKLK

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0022627 - cytosolic small ribosomal subunit
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0043024 - ribosomal small subunit binding
biological_process GO:0006417 - regulation of translation
GO:0044238 - primary metabolic process
GO:0017148 - negative regulation of translation
GO:0045900 - negative regulation of translational elongation
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Bubunenko M., et al., 2007
[2] Chen SS., et al., 2013
[3] Ueta M., et al., 2008
[4] Yoshida H., et al., 2009
External database links:  
DIP:
DIP-48273N
ECOCYC:
EG11681-MONOMER
ECOLIWIKI:
b3203
INTERPRO:
IPR003489
INTERPRO:
IPR036567
MODBASE:
P0AFX0
PDB:
6H58
PDB:
6H4N
PDB:
2RQL
PDB:
4V8H
PFAM:
PF02482
PRIDE:
P0AFX0
REFSEQ:
NP_417670
SMR:
P0AFX0
UNIPROT:
P0AFX0


Operon      
Name: yrbG-kdsDC-lptCAB-rpoN-hpf-ptsN-rapZ-npr         
Operon arrangement:
Transcription unit        Promoter
yrbG-kdsD
yrbG-kdsDC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
lptAB
lptAB
lptB-rpoN-hpf-ptsN-yhbJ
rpoN-hpf-ptsN-yhbJ-npr


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_3514 (cluster) 3345196 forward For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter TSS_3515 3345209 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3516 3345220 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3517 3345418 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3518 3345499 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3519 3345526 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3520 3345533 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3521 3345596 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3522 3345796 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3523 3345915 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3524 3346078 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3525 3346195 forward nd [RS-EPT-CBR] [5]


Evidence    

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



Reference(s)    

 [1] Bubunenko M., Baker T., Court DL., 2007, Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli., J Bacteriol 189(7):2844-53

 [2] Chen SS., Williamson JR., 2013, Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry., J Mol Biol 425(4):767-79

 [3] Ueta M., Ohniwa RL., Yoshida H., Maki Y., Wada C., Wada A., 2008, Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli., J Biochem 143(3):425-33

 [4] Yoshida H., Ueta M., Maki Y., Sakai A., Wada A., 2009, Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase., Genes Cells 14(2):271-80

 [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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