RegulonDB RegulonDB 10.8: Gene Form
   

lepA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lepA lepB rseC rseB anti-terminator terminator TSS_2868 (cluster) TSS_2868 (cluster) TSS_2867 TSS_2867 lepAp lepAp TSS_2866 TSS_2866 lepBp1 lepBp1

Gene      
Name: lepA    Texpresso search in the literature
Synonym(s): ECK2567, EG10529, b2569
Genome position(nucleotides): 2705325 <-- 2707124 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.72
External database links:  
ASAP:
ABE-0008452
CGSC:
18199
ECHOBASE:
EB0524
OU-MICROARRAY:
b2569
PortEco:
lepA
STRING:
511145.b2569
COLOMBOS: lepA


Product      
Name: 30S ribosomal subunit biogenesis factor LepA
Synonym(s): EF4, LepA, elongation factor 4
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,inner membrane
Molecular weight: 66.57
Isoelectric point: 5.258
Motif(s):
 
Type Positions Sequence
156 -> 185 TDAVRCSAKTGVGVQDVLERLVRDIPPPEG
487 -> 592 INGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQLRKNVLAKCYGGDISRKKKLLQKQKEGKKRMKQIGNVELPQEAFLAIL
2 -> 181 KNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIP
399 -> 482 LREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVR
266 -> 266 H

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
molecular_function GO:0003746 - translation elongation factor activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0043022 - ribosome binding
GO:0000166 - nucleotide binding
GO:0003924 - GTPase activity
GO:0005525 - GTP binding
GO:0042802 - identical protein binding
GO:0043023 - ribosomal large subunit binding
GO:0043024 - ribosomal small subunit binding
GO:0097216 - guanosine tetraphosphate binding
biological_process GO:0006412 - translation
GO:0006414 - translational elongation
GO:0009409 - response to cold
GO:0009268 - response to pH
GO:0009651 - response to salt stress
GO:0042274 - ribosomal small subunit biogenesis
GO:0045727 - positive regulation of translation
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Gibbs MR., et al., 2017
[2] Liu H., et al., 2011
[3] Liu H., et al., 2010
[4] Pech M., et al., 2011
[5] Qin Y., et al., 2006
[6] Sergiev PV., et al., 2012
[7] Woolstenhulme CJ., et al., 2013
[8] Xie P. 2013
[9] Zhang D., et al., 2012
External database links:  
DIP:
DIP-29868N
ECOCYC:
EG10529-MONOMER
ECOLIWIKI:
b2569
INTERPRO:
IPR000795
INTERPRO:
IPR038363
INTERPRO:
IPR035654
INTERPRO:
IPR035647
INTERPRO:
IPR031157
INTERPRO:
IPR027417
INTERPRO:
IPR013842
INTERPRO:
IPR006297
INTERPRO:
IPR005225
INTERPRO:
IPR004161
INTERPRO:
IPR000640
MINT:
MINT-1225739
MODBASE:
P60785
PANTHER:
PTHR23115:SF40
PDB:
3JCE
PDB:
3CB4
PDB:
3DEG
PDB:
3JCD
PFAM:
PF00679
PFAM:
PF00009
PFAM:
PF03144
PFAM:
PF06421
PRIDE:
P60785
PRINTS:
PR00315
PRODB:
PRO_000023079
PROSITE:
PS00301
PROSITE:
PS51722
REFSEQ:
NP_417064
SMART:
SM00838
SMR:
P60785
SWISSMODEL:
P60785
UNIPROT:
P60785


Operon      
Name: lepAB         
Operon arrangement:
Transcription unit        Promoter
lepAB


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 lepBp1 2705464 reverse Similarity to the consensus
Read more >
[ICWHO] [10]
  promoter TSS_2866 2706051 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_2867 2707204 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_2868 (cluster) 2707211 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [11]


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] Gibbs MR., Moon KM., Chen M., Balakrishnan R., Foster LJ., Fredrick K., 2017, Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome., Proc Natl Acad Sci U S A 114(5):980-985

 [2] Liu H., Chen C., Zhang H., Kaur J., Goldman YE., Cooperman BS., 2011, The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis., Proc Natl Acad Sci U S A 108(39):16223-8

 [3] Liu H., Pan D., Pech M., Cooperman BS., 2010, Interrupted catalysis: the EF4 (LepA) effect on back-translocation., J Mol Biol 396(4):1043-52

 [4] Pech M., Karim Z., Yamamoto H., Kitakawa M., Qin Y., Nierhaus KH., 2011, Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations., Proc Natl Acad Sci U S A 108(8):3199-203

 [5] Qin Y., Polacek N., Vesper O., Staub E., Einfeldt E., Wilson DN., Nierhaus KH., 2006, The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome., Cell 127(4):721-33

 [6] Sergiev PV., Golovina AY., Sergeeva OV., Osterman IA., Nesterchuk MV., Bogdanov AA., Dontsova OA., 2012, How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?, Nucleic Acids Res 40(12):5694-705

 [7] Woolstenhulme CJ., Parajuli S., Healey DW., Valverde DP., Petersen EN., Starosta AL., Guydosh NR., Johnson WE., Wilson DN., Buskirk AR., 2013, Nascent peptides that block protein synthesis in bacteria., Proc Natl Acad Sci U S A 110(10):E878-87

 [8] Xie P., 2013, Dynamics of forward and backward translocation of mRNA in the ribosome., PLoS One 8(8):e70789

 [9] Zhang D., Liu G., Xue J., Lou J., Nierhaus KH., Gong W., Qin Y., 2012, Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome., Nucleic Acids Res 40(21):10851-65

 [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

 [11] 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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