RegulonDB RegulonDB 11.1: Gene Form
   

thrS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

thrS arpB infC yniD NsrR DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp anti-anti-terminator anti-terminator terminator yniDp6 yniDp6 thrSp thrSp TSS_2036 TSS_2036 TSS_2035 TSS_2035 TSS_2034 TSS_2034 TSS_2033 (cluster) TSS_2033 (cluster) TSS_2032 TSS_2032 TSS_2031 TSS_2031 TSS_2030 TSS_2030 TSS_2029 TSS_2029 infCp1 infCp1 TSS_2027 TSS_2027 TSS_2026 TSS_2026 TSS_2025 (cluster) TSS_2025 (cluster) TSS_2024 TSS_2024 infCp2 infCp2 TSS_2023 TSS_2023 TSS_2022 TSS_2022 TSS_2021 TSS_2021 rpmIp rpmIp TSS_2020 (cluster) TSS_2020 (cluster)

Gene      
Name: thrS    Texpresso search in the literature
Synonym(s): ECK1717, EG11001, b1719
Genome position(nucleotides): 1800642 <-- 1802570
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.56
External database links:  
ASAP:
 ABE-0005736
CGSC:
 108
ECHOBASE:
 EB0994
ECOLIHUB:
 thrS
OU-MICROARRAY:
 b1719
STRING:
 511145.b1719
COLOMBOS: thrS


Product      
Name: threonine—tRNA ligase
Synonym(s): ThrRS, ThrS
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 74.014
Isoelectric point: 6.122
Motif(s):
 
Type Positions Sequence Comment
1 -> 61 MPVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIIT UniProt: TGS.
2 -> 241 PVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLEEAAK UniProt: N-terminal region which includes the editing domain, important for catalytic efficiency, its loss increases mischarging with L-serine, deacylation of incorrectly charged tRNA no longer occurs, partially complements a deletion strain; Sequence Annotation Type: region of interest.
4 -> 61 ITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIIT
63 -> 224 KDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWA UniProt: N2 domain, the editing domain; Sequence Annotation Type: region of interest.
73 -> 77 HSCAH UniProt: No longer edits mischarged L-seryl-tRNA(Thr), mischarges tRNA(Thr) with L-serine, correct acylation is unaffected..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.1 - amino acid -activation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0000900 - translation repressor activity, mRNA regulatory element binding
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0004812 - aminoacyl-tRNA ligase activity
GO:0004829 - threonine-tRNA ligase activity
GO:0003723 - RNA binding
GO:0000049 - tRNA binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008270 - zinc ion binding
GO:0042803 - protein homodimerization activity
GO:0048027 - mRNA 5'-UTR binding
GO:0002161 - aminoacyl-tRNA editing activity
biological_process GO:0106074 - aminoacyl-tRNA metabolism involved in translational fidelity
GO:0006412 - translation
GO:0006417 - regulation of translation
GO:0006418 - tRNA aminoacylation for protein translation
GO:0043039 - tRNA aminoacylation
GO:0045947 - negative regulation of translational initiation
GO:0006435 - threonyl-tRNA aminoacylation
GO:0046677 - response to antibiotic
Note(s): Note(s): ...[more].
Reference(s): [1] Arnez JG., et al., 2000
[2] Azam MS., et al., 2020
[3] Comer MM. 1981
[4] Dutta S., et al., 2019
[5] Duval M., et al., 2013
[6] Ehresmann B., et al., 1988
[7] Elhardt D., et al., 1982
[8] Elseviers D., et al., 1982
[9] Fayat G., et al., 1983
[10] Garoff L., et al., 2018
[11] Grull JM., et al., 1979
[12] Itikawa H., et al., 1989
[13] Johnson EJ., et al., 1977
[14] Kim CW., et al., 2007
[15] Mayaux JF., et al., 1983
[16] Nass G., et al., 1974
[17] Neidhardt FC., et al., 1977
[18] Nogueira T., et al., 2001
[19] Ny T., et al., 1980
[20] Plumbridge JA., et al., 1982
[21] Plumbridge JA., et al., 1982
[22] Plumbridge JA., et al., 1980
[23] Ruan B., et al., 2008
[24] Serina S., et al., 2004
[25] Springer M., et al., 1979
[26] Springer M., et al., 1982
[27] Theobald A., et al., 1988
[28] Thomale J., et al., 1975
[29] Thomale J., et al., 1977
[30] Thomale J., et al., 1978
[31] Thomale J., et al., 1972
[32] Torres-Larios A., et al., 2003
[33] Wada M., et al., 1986
[34] Wertheimer SJ., et al., 1988
[35] Wu TH., et al., 1984
[36] Zenkova M., et al., 1995
External database links:  
ALPHAFOLD:
 P0A8M3
DIP:
 DIP-35823N
ECOCYC:
 THRS-MONOMER
ECOLIWIKI:
 b1719
INTERPRO:
 IPR002314
INTERPRO:
 IPR018163
INTERPRO:
 IPR012947
INTERPRO:
 IPR033728
INTERPRO:
 IPR002320
INTERPRO:
 IPR004095
INTERPRO:
 IPR004154
INTERPRO:
 IPR006195
INTERPRO:
 IPR012675
INTERPRO:
 IPR012676
INTERPRO:
 IPR036621
MINT:
 P0A8M3
MODBASE:
 P0A8M3
PANTHER:
 PTHR11451
PDB:
 4P3P
PDB:
 4P3O
PDB:
 4HWS
PDB:
 4HWR
PDB:
 4HWP
PDB:
 4HWO
PDB:
 1TKY
PDB:
 1TKG
PDB:
 1TKE
PDB:
 1TJE
PDB:
 1QF6
PDB:
 1KOG
PDB:
 1FYF
PDB:
 1EVK
PDB:
 1EVL
PFAM:
 PF02824
PFAM:
 PF03129
PFAM:
 PF00587
PFAM:
 PF07973
PRIDE:
 P0A8M3
PRINTS:
 PR01047
PRODB:
 PRO_000024069
PROSITE:
 PS51880
PROSITE:
 PS50862
REFSEQ:
 NP_416234
SMART:
 SM00863
SMR:
 P0A8M3
UNIPROT:
 P0A8M3


Operon      
Name: thrS-infC-rpmI-rplT-pheMST-ihfA         
Operon arrangement:
Transcription unit        Promoter
ihfA
pheM
pheMST-ihfA
rplT
rplT-pheM
rpmI-rplT
infC-rpmI-rplT
infC
thrS-infC
thrS-infC-rpmI-rplT-pheMST-ihfA


Transcriptional Regulation      
Display Regulation             
Repressed by: NsrR


RNA cis-regulatory element    
Attenuation: Translational


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_2020 (cluster) 1800331 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2021 1800430 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2022 1800596 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2023 1800817 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2024 1800819 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2025 (cluster) 1801170 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2026 1801273 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2027 1801278 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2029 1801426 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2030 1801552 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2031 1801633 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2032 1802563 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2033 (cluster) 1802626 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2034 1802634 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2035 1802637 reverse nd [RS-EPT-CBR] [37]
  promoter TSS_2036 1802699 reverse nd [RS-EPT-CBR] [37]
  promoter yniDp6 1805101 forward nd [COMP-AINF] [38]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Arnez JG., Sankaranarayanan R., Dock-Bregeon AC., Francklyn CS., Moras D., 2000, Aminoacylation at the Atomic Level in Class IIa Aminoacyl-tRNA Synthetases., J Biomol Struct Dyn 17 Suppl 1:23-7

 [2] Azam MS., Vanderpool CK., 2020, Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer., Mol Microbiol 114(3):391-408

 [3] Comer MM., 1981, Gene organization around the phenylalanyl-transfer ribonucleic acid synthetase locus in Escherichia coli., J Bacteriol 146(1):269-74

 [4] Dutta S., Nandi N., 2019, Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate., J Biomol Struct Dyn 37(2):336-358

 [5] Duval M., Korepanov A., Fuchsbauer O., Fechter P., Haller A., Fabbretti A., Choulier L., Micura R., Klaholz BP., Romby P., Springer M., Marzi S., 2013, Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation., PLoS Biol 11(12):e1001731

 [6] Ehresmann B., Moine H., Romby P., Springer M., Grunberg-Manago M., Ebel JP., Ehresmann C., 1988, Secondary structure of the Escherichia coli translational operator of threonyl-tRNA synthetase and relationship to its function., Gene 72(1-2):187-8

 [7] Elhardt D., Wirth R., Bock A., 1982, Regulation of formation of threonyl-tRNA synthetase, phenylalanyl-tRNA synthetase and protein synthesis initiation factor 3 from Escherichia coli in vivo and in vitro., Eur J Biochem 123(3):477-82

 [8] Elseviers D., Gallagher P., Hoffman A., Weinberg B., Schwartz I., 1982, Molecular cloning and regulation of expression of the genes for initiation factor 3 and two aminoacyl-tRNA synthetases., J Bacteriol 152(1):357-62

 [9] Fayat G., Fromant M., Kalogerakos T., Blanquet S., 1983, Effect of the overproduction of phenylalanyl- and threonyl-tRNA synthetases on tRNAPhe and tRNAThr concentrations in E. coli cells., Biochimie 65(3):221-5

 [10] Garoff L., Huseby DL., Praski Alzrigat L., Hughes D., 2018, Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli., J Antimicrob Chemother 73(12):3285-3292

 [11] Grull JM., Hennecke H., Frohler J., Thomale J., Nass G., Bock A., 1979, Escherichia coli mutants overproducing phenylalanyl- and threonyl-tRNA synthetase., J Bacteriol 137(1):480-9

 [12] Itikawa H., Wada M., Sekine K., Fujita H., 1989, Phosphorylation of glutaminyl-tRNA synthetase and threonyl-tRNA synthetase by the gene products of dnaK and dnaJ in Escherichia coli K-12 cells., Biochimie 71(9-10):1079-87

 [13] Johnson EJ., Cohen GN., Saint-Girons I., 1977, Threonyl-transfer ribonucleic acid synthetase and the regulation of the threonine operon in Escherichia coli., J Bacteriol 129(1):66-70

 [14] Kim CW., Han KS., Ryu KS., Kim BH., Kim KH., Choi SI., Seong BL., 2007, N-terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers., Protein Sci 16(4):635-43

 [15] Mayaux JF., Fayat G., Fromant M., Springer M., Grunberg-Manago M., Blanquet S., 1983, Structural and transcriptional evidence for related thrS and infC expression., Proc Natl Acad Sci U S A 80(20):6152-6

 [16] Nass G., Thomale J., 1974, Alteration of structure of level of threonyl-tRNA-synthetase in Borrelidin resistant mutants of E. coli., FEBS Lett 39(2):182-6

 [17] Neidhardt FC., Bloch PL., Pedersen S., Reeh S., 1977, Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli., J Bacteriol 129(1):378-87

 [18] Nogueira T., de Smit M., Graffe M., Springer M., 2001, The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene., J Mol Biol 310(4):709-22

 [19] Ny T., Thomale J., Hjalmarsson K., Nass G., Bjork GR., 1980, Non-coordinate regulation of enzymes involved in transfer RNA metabolism in Escherichia coli., Biochim Biophys Acta 607(2):277-84

 [20] Plumbridge JA., Springer M., 1982, Escherichia coli phenylalanyl-tRNA synthetase operon: transcription studies of wild-type and mutated operons on multicopy plasmids., J Bacteriol 152(2):661-8

 [21] Plumbridge JA., Springer M., 1982, Escherichia coli phenylalanyl-tRNA synthetase operon: characterization of mutations isolated on multicopy plasmids., J Bacteriol 152(2):650-60

 [22] Plumbridge JA., Springer M., Graffe M., Goursot R., Grunberg-Manago M., 1980, Physical localisation and cloning of the structural gene for E. coli initiation factor IF3 from a group of genes concerned with translation., Gene 11(1-2):33-42

 [23] Ruan B., Palioura S., Sabina J., Marvin-Guy L., Kochhar S., Larossa RA., Soll D., 2008, Quality control despite mistranslation caused by an ambiguous genetic code., Proc Natl Acad Sci U S A 105(43):16502-7

 [24] Serina S., Nozza F., Nicastro G., Faggioni F., Mottl H., Deho G., Polissi A., 2004, Scanning the Escherichia coli chromosome by random transposon mutagenesis and multiple phenotypic screening., Res Microbiol 155(8):692-701

 [25] Springer M., Graffe M., Grunberg-Manago M., 1979, Genetic organization of the E. coli chromosome around the structural gene for initiation factor IF3 (infC)., Mol Gen Genet 169(3):337-43

 [26] Springer M., Plumbridge JA., Trudel M., Graffe M., Grunberg-Manago M., 1982, Transcription units around the gene for E. coli translation initiation factor IF3 (infC)., Mol Gen Genet 186(2):247-52

 [27] Theobald A., Springer M., Grunberg-Manago M., Ebel JP., Giege R., 1988, Tertiary structure of Escherichia coli tRNA(3Thr) in solution and interaction of this tRNA with the cognate threonyl-tRNA synthetase., Eur J Biochem 175(3):511-24

 [28] Thomale J., Nass G., 1975, Change of isoaccepting threonyl-tRNA and contitutively increased level of threonyl-tRNA-synthetase in E. coli., FEBS Lett 56(1):111-4

 [29] Thomale J., Nass G., 1977, Genetically determined differences in concentrations of isoaccepting tRNAs in Escherichia coli., Nucleic Acids Res 4(12):4313-22

 [30] Thomale J., Nass G., 1978, Alteration of the intracellular concentration of aminoacyl-tRNA synthetases and isoaccepting tRNAs during amino-acid limited growth in Escherichia coli., Eur J Biochem 85(2):407-18

 [31] Thomale J., Nass G., 1972, [Regulation of threonyl-tRNA synthetase formation in borrelidin resistent E. coli mutants]., Hoppe Seylers Z Physiol Chem 353(10):1572

 [32] Torres-Larios A., Sankaranarayanan R., Rees B., Dock-Bregeon AC., Moras D., 2003, Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase., J Mol Biol 331(1):201-11

 [33] Wada M., Sekine K., Itikawa H., 1986, Participation of the dnaK and dnaJ gene products in phosphorylation of glutaminyl-tRNA synthetase and threonyl-tRNA synthetase of Escherichia coli K-12., J Bacteriol 168(1):213-20

 [34] Wertheimer SJ., Klotsky RA., Schwartz I., 1988, Transcriptional patterns for the thrS-infC-rplT operon of Escherichia coli., Gene 63(2):309-20

 [35] Wu TH., Wood DL., Stein PL., Comer MM., 1984, Transcription of a gene cluster coding for two aminoacyl-tRNA synthetases and an initiation factor in Escherichia coli., J Mol Biol 173(2):177-209

 [36] Zenkova M., Ehresmann C., Caillet J., Springer M., Karpova G., Ehresmann B., Romby P., 1995, A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex., Eur J Biochem 231(3):726-35

 [37] 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.

 [38] 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

RegulonDB