RegulonDB RegulonDB 11.0: Gene Form
   

greB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhgF ompR greB envZ IHF CRP IHF IHF  OmrB  OmrA TSS_4005 (cluster) TSS_4005 (cluster) TSS_4004 TSS_4004 yhgFp2 yhgFp2 greBp7 greBp7 ompRp4 ompRp4 greBp8 greBp8 ompRp1 ompRp1 ompRp2 ompRp2 ompRp3 ompRp3 TSS_4002 TSS_4002 TSS_4001 TSS_4001

Gene      
Name: greB    Texpresso search in the literature
Synonym(s): ECK3393, EG11578, b3406
Genome position(nucleotides): 3536812 --> 3537288
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.9
External database links:  
ASAP:
ABE-0011117
CGSC:
35448
ECHOBASE:
EB1538
ECOLIHUB:
greB
OU-MICROARRAY:
b3406
STRING:
511145.b3406
COLOMBOS: greB


Product      
Name: transcription elongation factor GreB
Synonym(s): GreB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 18.527
Isoelectric point: 8.361
Motif(s):
 
Type Positions Sequence Comment
6 -> 74 VTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCLENLKI
81 -> 155 QEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEY

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0070063 - RNA polymerase binding
biological_process GO:0006352 - DNA-templated transcription, initiation
GO:0032784 - regulation of DNA-templated transcription, elongation
GO:0006354 - DNA-templated transcription, elongation
GO:0031439 - positive regulation of mRNA cleavage
Note(s): Note(s): ...[more].
Evidence: [IE] Inferred from experiment
Reference(s): [1] Altmann CR., et al., 1994
[2] Borukhov S., et al., 1996
[3] Hung SC., et al., 1997
[4] Koulich D., et al., 1998
[5] Orlova M., et al., 1995
[6] Trautinger BW., et al., 2002
[7] Wang D., et al., 1997
[8] Zakharova N., et al., 1998
External database links:  
ALPHAFOLD:
P30128
DIP:
DIP-9834N
ECOCYC:
EG11578-MONOMER
ECOLIWIKI:
b3406
INTERPRO:
IPR036805
INTERPRO:
IPR018151
INTERPRO:
IPR006358
INTERPRO:
IPR001437
INTERPRO:
IPR023459
INTERPRO:
IPR028624
INTERPRO:
IPR036953
INTERPRO:
IPR022691
MODBASE:
P30128
PANTHER:
PTHR30437
PDB:
2P4V
PDB:
6RI7
PDB:
6RIN
PFAM:
PF01272
PFAM:
PF03449
PRIDE:
P30128
PRODB:
PRO_000022837
PROSITE:
PS00830
PROSITE:
PS00829
REFSEQ:
YP_026216
SMR:
P30128
UNIPROT:
P30128


Operon      
Name: greB         
Operon arrangement:
Transcription unit        Promoter
greB


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_4001 3536371 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_4002 3536377 reverse nd [RS-EPT-CBR] [9]
  promoter greBp8 3536744 forward nd [ICWHO] [10]
  promoter greBp7 3536780 forward nd [ICWHO] [10]
  promoter yhgFp2 3537176 forward nd [ICWHO] [10]
  promoter TSS_4004 3537268 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4005 (cluster) 3537353 forward nd [RS-EPT-CBR] [9]


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] Altmann CR., Solow-Cordero DE., Chamberlin MJ., 1994, RNA cleavage and chain elongation by Escherichia coli DNA-dependent RNA polymerase in a binary enzyme.RNA complex., Proc Natl Acad Sci U S A 91(9):3784-8

 [2] Borukhov S., Goldfarb A., 1996, Purification and assay of Escherichia coli transcript cleavage factors GreA and GreB., Methods Enzymol 274:315-26

 [3] Hung SC., Gottesman ME., 1997, The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coli RNA polymerase without abolishing its catalytic activities., Genes Dev 11(20):2670-8

 [4] Koulich D., Nikiforov V., Borukhov S., 1998, Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor., J Mol Biol 276(2):379-89

 [5] Orlova M., Newlands J., Das A., Goldfarb A., Borukhov S., 1995, Intrinsic transcript cleavage activity of RNA polymerase., Proc Natl Acad Sci U S A 92(10):4596-600

 [6] Trautinger BW., Lloyd RG., 2002, Modulation of DNA repair by mutations flanking the DNA channel through RNA polymerase., EMBO J 21(24):6944-53

 [7] Wang D., Landick R., 1997, Nuclease cleavage of the upstream half of the nontemplate strand DNA in an Escherichia coli transcription elongation complex causes upstream translocation and transcriptional arrest., J Biol Chem 272(9):5989-94

 [8] Zakharova N., Bass I., Arsenieva E., Nikiforov V., Severinov K., 1998, Mutations in and monoclonal antibody binding to evolutionary hypervariable region of Escherichia coli RNA polymerase beta' subunit inhibit transcript cleavage and transcript elongation., J Biol Chem 273(38):24912-20

 [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.

 [10] 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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