|Gene:||pheS||Accession Numbers: EG10709 (EcoCyc), b1714, ECK1712|
Component of: phenylalanyl-tRNA synthetase (extended summary available)
The α subunit of PheRS contains the phenylalanine binding site [Hennecke75, Lavrik82] within the conserved motif 2 and motif 3 of the protein [Kast91, Kast91a]. It interacts with the 3'-adenosine of tRNAPhe [Hountondji87].
Isolated α subunits exist primarily as dimers [Bobkova91].
|Map Position: [1,795,983 <- 1,796,966] (38.71 centisomes, 139°)||Length: 984 bp / 327 aa|
Molecular Weight of Polypeptide: 36.832 kD (from nucleotide sequence), 38 kD (experimental) [Ducruix83]
Unification Links: ASAP:ABE-0005722, CGSC:400, DIP:DIP-6878N, EchoBASE:EB0703, EcoGene:EG10709, EcoliWiki:b1714, Mint:MINT-1229741, ModBase:P08312, OU-Microarray:b1714, PortEco:pheS, Pride:P08312, Protein Model Portal:P08312, RefSeq:NP_416229, RegulonDB:EG10709, SMR:P08312, String:511145.b1714, Swiss-Model:P08312, UniProt:P08312
Relationship Links: InterPro:IN-FAMILY:IPR002319, InterPro:IN-FAMILY:IPR004188, InterPro:IN-FAMILY:IPR004529, InterPro:IN-FAMILY:IPR006195, InterPro:IN-FAMILY:IPR010978, InterPro:IN-FAMILY:IPR022911, Pfam:IN-FAMILY:PF01409, Pfam:IN-FAMILY:PF02912, Prosite:IN-FAMILY:PS50862
|MultiFun Terms:||information transfer → protein related → amino acid -activation|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Subunit of: phenylalanyl-tRNA synthetase
Subunit composition of
phenylalanyl-tRNA synthetase = [PheS]2[PheT]2
phenylalanyl-tRNA synthetase α-chain = PheS (summary available)
phenylalanyl-tRNA synthetase β-chain = PheT (summary available)
Phenylalanyl-tRNA synthetase (PheRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. PheRS belongs to the Class IIC aminoacyl tRNA synthetases [Eriani90, Cusack91, Perona12].
PheRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic activity [Fayat74, Ducruix83]. Two molecules of tRNAPhe bind to one PheRS complex [Dessen83], and both binding sites are active sites [Bartmann75, Hennecke76]. Binding is not dependent on Mg2+ [Krauss75]. A crystal structure of PheRS in a complex with phenylalanine and AMP has been solved at 3.05 Å resolution, revealing structural differences between the E. coli and T. thermophilus enzymes [Mermershtain11].
The reaction mechanism of PheRS includes the formation of an aminoacyl adenylate intermediate, which then serves as the animo acid donor in the aminoacyl-tRNA synthetase reaction [Lagerkvist77]. Binding of tRNAPhe to PheRS induces a conformational change in the tRNA [Favre79] as well as in PheRS [Holler81]. Aminoacylation is limited by the kinetics of a conformational change of the PheRS-Phe-tRNAPhe complex [Baltzinger82, Baltzinger82a]. PheRS can aminoacylate a synthetic substrate with a deoxyribose backbone (tDNA) [Khan88b].
Specificity determinants within tRNAPhe that are important for recognition by PheRS, for attenuation, and for editing have been identified [Ankilova75, Vlassov78, Vacher85, Delamarche87, Wilson89, Pages90, Pallanck91, Peterson92, Peterson93, Moor94, Peterson94, Ling07]. A synthetically constructed tRNAPhe(AAA) is not a good substrate for PheRS [Gavini92]. Specificity determinants and residues within PheRS that are important for catalytic activity have been investigated [Hountondji87]. The Ala294 residue of the α subunit is involved in binding phenylalanine and influences amino acid specificity by determining of the size of the binding pocket [Ibba94].
A proofreading mechanism hydrolyzes a PheRS-tyrosine adenylate complex and Tyr-tRNAPhe [Ibba94, Roy04a]. The editing site localizes to the B3/B4 domain of the β subunit [Roy04a]. PheRS of E. coli B contains a proofreading activity which deacylates misacylated Ile-tRNAPhe [Yarus72, Gabius83]. The post-transfer editing activity of PheRS is not essential for growth, but it is required for survival under oxidative stress conditions. This may be due to its ability to edit meta-tyrosine, a metabolic byproduct of the oxidation of phenylalanine [Bullwinkle14].
A mutant with temperature-sensitive PheRS was isolated [Eidlic65].
PheRS is an antimicrobial drug target. Phenyl-thiazolylurea-sulfonamides act by inhibiting PheRS; novel inhibitors of the enzyme have been isolated [Abibi14].
Molecular Weight: 250 kD (experimental) [Ducruix83]
Enzymatic reaction of: phenylalanyl-tRNA synthetase
EC Number: 188.8.131.52a tRNAphe + L-phenylalanine + ATP + H+ → an L-phenylalanyl-[tRNAphe] + AMP + diphosphate
The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.
The reaction is physiologically favored in the direction shown.
In Pathways: tRNA charging
Equilibrium constants at various Mg2+ concentrations have been measured [Airas07].
|Substrate||Km (μM)||kcat (sec-1)||kcat/Km (sec-1 μM-1)||Citations|
|a tRNAphe||2.2, 2.7||0.077, 0.82||[Roy06, BRENDA14]|
|Pfam PF02912||17 -> 87|
|Pfam PF01409||92 -> 326|
10/20/97 Gene b1714 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10709; confirmed by SwissProt match.
Abibi14: Abibi A, Ferguson AD, Fleming PR, Gao N, Hajec LI, Hu J, Laganas VA, McKinney DC, McLeod SM, Prince DB, Shapiro AB, Buurman ET (2014). "The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability." J Biol Chem 289(31);21651-62. PMID: 24936059
Ankilova75: Ankilova VN, Vlassov VV, Knorre DG, Melamed NV, Nuzdihna NA (1975). "Involvement of the D-stem of tRNAPhe (E. coli) in interaction with phenylalanyl-tRNA synthetase as shown by chemical modification." FEBS Lett 60(1);168-71. PMID: 776674
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Baltzinger82: Baltzinger M, Holler E (1982). "Kinetics of acyl transfer ribonucleic acid complexes of Escherichia coli phenylalanyl-tRNA synthetase. A conformational change is rate limiting in catalysis." Biochemistry 21(10);2460-7. PMID: 7046786
Baltzinger82a: Baltzinger M, Holler E (1982). "Catalytic mechanism of phenylalanyl-tRNA synthetase of Escherichia coli K10. Conformational change and tRNAPhe phenylalanylation are concerted." Biochemistry 21(10);2467-76. PMID: 7046787
Bartmann75a: Bartmann P, Hanke T, Holler E (1975). "L-phenylalanine:tRNA ligase of Escherichia coli K10. A rapid kinetic investigation of the catalytic reaction." Biochemistry 14(22);4777-86. PMID: 1101957
Beyer04: Beyer D, Kroll HP, Endermann R, Schiffer G, Siegel S, Bauser M, Pohlmann J, Brands M, Ziegelbauer K, Haebich D, Eymann C, Brotz-Oesterhelt H (2004). "New class of bacterial phenylalanyl-tRNA synthetase inhibitors with high potency and broad-spectrum activity." Antimicrob Agents Chemother 48(2);525-32. PMID: 14742205
Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503
Bobkova91: Bobkova EV, Mashanov-Golikov AV, Wolfson A, Ankilova VN, Lavrik OI (1991). "Comparative study of subunits of phenylalanyl-tRNA synthetase from Escherichia coli and Thermus thermophilus." FEBS Lett 290(1-2);95-8. PMID: 1915899
Bobkova92: Bobkova EV, Stepanov VG, Lavrik OI (1992). "A comparative study of the relationship between thermostability and function of phenylalanyl-tRNA synthetases from Escherichia coli and Thermus thermophilus." FEBS Lett 302(1);54-6. PMID: 1587354
Bullwinkle14: Bullwinkle T, Reynolds NM, Raina M, Moghal AB, Matsa E, Rajkovic A, Kayadibi H, Fazlollahi F, Ryan C, Howitz N, Faull KF, Lazazzera B, Ibba M (2014). "Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code." Elife ;e02501. PMID: 24891238
Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043
Delamarche87: Delamarche C, Vacher J, Buckingham RH (1987). "Mutants affecting tRNA(Phe) from Escherichia coli. Studies of the suppression of thermosensitive phenylalanyl-tRNA synthetase." Eur J Biochem 168(2);365-9. PMID: 3311746
Dessen83: Dessen P, Ducruix A, Hountondji C, May RP, Blanquet S (1983). "Neutron scattering study of the binding of tRNAPhe to Escherichia coli phenylalanyl-tRNA synthetase." Biochemistry 22(2);281-4. PMID: 6337625
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Ducruix83: Ducruix A, Hounwanou N, Reinbolt J, Boulanger Y, Blanquet S (1983). "Purification and reversible subunit dissociation of overproduced Escherichia coli phenylalanyl-tRNA synthetase." Biochim Biophys Acta 741(2);244-50. PMID: 6360212
Eidlic65: Eidlic L, Neidhardt FC (1965). "Protein and nucleic acid synthesis in two mutants of Escherichia coli with temperature-sensitive aminoacyl ribonucleic acid synthetases." J Bacteriol 89;706-11. PMID: 14273649
Eriani90: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971
Fayat74: Fayat G, Blanquet S, Dessen P, Batelier G, Waller JP (1974). "The molecular weight and subunit composition of phenylalanyl-tRNA synthetase from Escherichia coli K-12." Biochimie 56(1);35-41. PMID: 4603142
Fayat83: Fayat G, Mayaux JF, Sacerdot C, Fromant M, Springer M, Grunberg-Manago M, Blanquet S (1983). "Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20." J Mol Biol 171(3);239-61. PMID: 6317865
Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371
Gabius82: Gabius HJ, Freist W, Cramer F (1982). "Phenylalanyl-tRNA synthetases from hen liver cytoplasm and mitochondria, yeast cytoplasm and mitochondria, and from Escherichia coli: substrate specificity relationship with regard to ATP analogs." Hoppe Seylers Z Physiol Chem 363(10);1241-6. PMID: 6754571
Gabius83: Gabius HJ, von der Haar F, Cramer F (1983). "Evolutionary aspects of accuracy of phenylalanyl-tRNA synthetase. A comparative study with enzymes from Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, and turkey liver using phenylalanine analogues." Biochemistry 22(10);2331-9. PMID: 6222761
Gavini92: Gavini N, Pulakat L (1992). "The tRNA species for redundant genetic codons NNU and NNC. A thought on the absence of phenylalanine tRNA with AAA anticodon in Escherichia coli." J Biol Chem 267(4);2240-3. PMID: 1370814
Hennecke75: Hennecke H, Bock A (1975). "Altered alpha subunits in phenylalanyl-tRNA synthetases from p-fluorophenylalanine-resistant strains of Escherichis coli." Eur J Biochem 55(2);431-7. PMID: 1104359
Holler81: Holler E, Wang CC, Ford NC (1981). "Detection of ligand-induced conformational changes in phenylalanyl-tRNA synthetase of Escherichia coli K10 by laser light scattering." Biochemistry 20(4);861-7. PMID: 7011376
Hountondji87: Hountondji C, Schmitter JM, Beauvallet C, Blanquet S (1987). "Affinity labeling of Escherichia coli phenylalanyl-tRNA synthetase at the binding site for tRNAPhe." Biochemistry 26(17);5433-9. PMID: 2823880
Ibba94: Ibba M, Kast P, Hennecke H (1994). "Substrate specificity is determined by amino acid binding pocket size in Escherichia coli phenylalanyl-tRNA synthetase." Biochemistry 33(23);7107-12. PMID: 8003476
Kast91a: Kast P, Wehrli C, Hennecke H (1991). "Impaired affinity for phenylalanine in Escherichia coli phenylalanyl-tRNA synthetase mutant caused by Gly-to-Asp exchange in motif 2 of class II tRNA synthetases." FEBS Lett 293(1-2);160-3. PMID: 1959653
Krauss75: Krauss G, Pingoud A, Boehme D, Riesner D, Peters F, Maas G (1975). "Equivalent and non-equivalent binding sites for +RNA on aminoacyl-tRNA synthetases." Eur J Biochem 55(3);517-29. PMID: 1100384
Lagerkvist77: Lagerkvist U, Akesson B, Branden R (1977). "Aminoacyl adenylate, a normal intermediate or a dead end in aminoacylation of transfer ribonucleic acid." J Biol Chem 252(3);1002-6. PMID: 320199
Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726
Lavrik82: Lavrik OI, Moor NA, Khodyreva SN (1982). "Phenylalanyl-tRNA synthetase from E. coli MRE-600: localization of the phenylalanine binding sites on the subunits by affinity reagents." Mol Biol Rep 8(2);123-6. PMID: 7043240
LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532
Mayaux81: Mayaux JF, Blanquet S (1981). "Binding of zinc to Escherichia coli phenylalanyl transfer ribonucleic acid synthetase. Comparison with other aminoacyl transfer ribonucleic acid synthetases." Biochemistry 20(16);4647-54. PMID: 6794600
Mayaux85: Mayaux JF, Fayat G, Panvert M, Springer M, Grunberg-Manago M, Blanquet S (1985). "Control of phenylalanyl-tRNA synthetase genetic expression. Site-directed mutagenesis of the pheS, T operon regulatory region in vitro." J Mol Biol 184(1);31-44. PMID: 3162032
Mermershtain11: Mermershtain I, Finarov I, Klipcan L, Kessler N, Rozenberg H, Safro MG (2011). "Idiosyncrasy and identity in the prokaryotic Phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP." Protein Sci 20(1);160-7. PMID: 21082706
Moor94: Moor NA, Repkova MN, Yamkovoy VI, Lavrik OI (1994). "Alterations at the 3'-CCA end of Escherichia coli and Thermus thermophilus tRNA(Phe) do not abolish their acceptor activity." FEBS Lett 351(2);241-2. PMID: 8082771
Pages90: Pages D, Buckingham RH (1990). "Mutants of pheV in Escherichia coli affecting control by attenuation of the pheS, T and pheA operons. Two distinct mechanisms for de-attenuation." J Mol Biol 216(1);17-24. PMID: 2231729
Pallanck91: Pallanck L, Schulman LH (1991). "Anticodon-dependent aminoacylation of a noncognate tRNA with isoleucine, valine, and phenylalanine in vivo." Proc Natl Acad Sci U S A 88(9);3872-6. PMID: 2023934
Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554
Reynolds10: Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P, Ibba M (2010). "Cell-specific differences in the requirements for translation quality control." Proc Natl Acad Sci U S A 107(9);4063-8. PMID: 20160120
Roy06: Roy H, Ibba M (2006). "Phenylalanyl-tRNA synthetase contains a dispensable RNA-binding domain that contributes to the editing of noncognate aminoacyl-tRNA." Biochemistry 45(30);9156-62. PMID: 16866361
Springer83: Springer M, Trudel M, Graffe M, Plumbridge J, Fayat G, Mayaux JF, Sacerdot C, Blanquet S, Grunberg-Manago M (1983). "Escherichia coli phenylalanyl-tRNA synthetase operon is controlled by attenuation in vivo." J Mol Biol 171(3);263-79. PMID: 6317866
Springer85a: Springer M, Mayaux JF, Fayat G, Plumbridge JA, Graffe M, Blanquet S, Grunberg-Manago M (1985). "Attenuation control of the Escherichia coli phenylalanyl-tRNA synthetase operon." J Mol Biol 181(4);467-78. PMID: 3158742
Springer87: Springer M, Graffe M, Mayaux JF, Dardel F, Fayat G, Blanquet S, Grunberg-Manago M (1987). "Open reading frames in the control regions of the phenylalanyl-tRNA synthetase operon of E. coli." Biochimie 69(10);1065-70. PMID: 3126825
Trudel84: Trudel M, Springer M, Graffe M, Fayat G, Blanquet S, Grunberg-Manago M (1984). "Regulation of E.coli phenylalanyl-tRNA synthetase operon in vivo." Biochim Biophys Acta 782(1);10-7. PMID: 6426518
Vlassov78: Vlassov VV, Khodyreva SN (1978). "Equilibrium screening-dialysis investigation of the nucleotide sequences in the tRNAPhe recognized by phenylalanyl-tRNA synthetase (Escherichia coli)." FEBS Lett 96(1);95-8. PMID: 365576
Wilson89: Wilson RK, Roe BA (1989). "Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA." Proc Natl Acad Sci U S A 86(2);409-13. PMID: 2643111
Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902
Lesage90: Lesage P, Truong HN, Graffe M, Dondon J, Springer M (1990). "Translated translational operator in Escherichia coli. Auto-regulation in the infC-rpmI-rplT operon." J Mol Biol 213(3);465-75. PMID: 2191140
Mayaux83: 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. PMID: 6353409
Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291
Springer86: Springer M, Graffe M, Butler JS, Grunberg-Manago M (1986). "Genetic definition of the translational operator of the threonine-tRNA ligase gene in Escherichia coli." Proc Natl Acad Sci U S A 83(12);4384-8. PMID: 3086882
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