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Escherichia coli K-12 substr. MG1655 Enzyme: 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)

Summary:
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) [Khan88].

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, Roy04]. The editing site localizes to the B3/B4 domain of the β subunit [Roy04]. 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].

Expression of pheST is derepressed by an attenuation mechanism when the level of aminoacylated tRNAPhe is low [Fayat83, Springer83, Trudel84, Springer87] and by high levels of PheRS [Springer85].

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].

Reviews: [Ibba00, Perona12]

Citations: [Bartmann75a]

Molecular Weight: 250 kD (experimental) [Ducruix83 ]

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006432 - phenylalanyl-tRNA aminoacylation Inferred from experiment [Comer76]
Molecular Function: GO:0004826 - phenylalanine-tRNA ligase activity Inferred from experiment [Fayat74]

Credits:
Last-Curated ? 01-Jul-2014 by Keseler I , SRI International


Enzymatic reaction of: phenylalanyl-tRNA synthetase

Synonyms: PheRS

EC Number: 6.1.1.20

tRNAphe + L-phenylalanine + ATP + H+ <=> L-phenylalanyl-tRNAphe + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Summary:
Equilibrium constants at various Mg2+ concentrations have been measured [Airas07].

Cofactors or Prosthetic Groups: Mg2+ [Airas96, Favre79]

Inhibitors (Competitive): 3-phenylpropanoate [Mulivor73] , phenyl-thiazolylurea-sulfonamides [Beyer04] , N-benzylbenzamidine [Danenberg75] , benzylguanidine [Danenberg75] , 2-phenylacetamidine [Danenberg75] , phenylalaninol [Mulivor73] , benzyl alcohol [Mulivor73]

Inhibitors (Unknown Mechanism): Zn2+ [Mayaux81]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
ATP
9.0
[Gabius82, BRENDA14]
ATP
130.0
[Hecht74]
tRNAphe
0.22
[Peterson92]
tRNAphe
2.2, 2.7
0.077, 0.82
[Roy06, BRENDA14]
L-phenylalanine
3.2
[Hecht74]
L-phenylalanine
5.3
3.34
[Roy06, BRENDA14]
L-phenylalanine
2.0
199.0
[Reynolds10, BRENDA14]

T(opt): 43 °C [BRENDA14, Bobkova92]


Subunit of phenylalanyl-tRNA synthetase: phenylalanyl-tRNA synthetase α-chain

Synonyms: PheS

Gene: pheS Accession Numbers: EG10709 (EcoCyc), b1714, ECK1712

Locations: cytosol

Sequence Length: 327 AAs

Molecular Weight: 36.832 kD (from nucleotide sequence)

Molecular Weight: 38 kD (experimental) [Ducruix83]

GO Terms:

Biological Process: GO:0006432 - phenylalanyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Eidlic65]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01]
GO:0043039 - tRNA aminoacylation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Lasserre06, Butland05]
GO:0000049 - tRNA binding Inferred by computational analysis [GOA01]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004826 - phenylalanine-tRNA ligase activity Inferred by computational analysis [GOA06, GOA01a, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01, Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0009328 - phenylalanine-tRNA ligase complex Inferred from experiment [Fayat74]

MultiFun Terms: information transfer protein related amino acid -activation

Unification Links: DIP:DIP-6878N , EcoliWiki:b1714 , Mint:MINT-1229741 , ModBase:P08312 , Pride:P08312 , Protein Model Portal:P08312 , RefSeq:NP_416229 , 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

Summary:
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].

The pheS5 mutant allele causes temperature-sensitive PheRS activity [Eidlic65, Kast92]. Intragenic supressors of the pheS5 mutation have been isolated and analyzed [Ponmani14].

Citations: [Comer76]

Essentiality data for pheS knockouts: ?

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: phenylalanyl-tRNA synthetase β-chain

Synonyms: PheT

Gene: pheT Accession Numbers: EG10710 (EcoCyc), b1713, ECK1711

Locations: cytosol, membrane

Sequence Length: 795 AAs

Molecular Weight: 87.378 kD (from nucleotide sequence)

Molecular Weight: 98 kD (experimental) [Ducruix83]

GO Terms:

Biological Process: GO:0006432 - phenylalanyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Comer76]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0008033 - tRNA processing Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Lasserre06, Butland05]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06, GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11]
GO:0004826 - phenylalanine-tRNA ligase activity Inferred by computational analysis [GOA06, GOA01a, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0009328 - phenylalanine-tRNA ligase complex Inferred from experiment [Fayat74]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: information transfer protein related amino acid -activation

Unification Links: DIP:DIP-6879N , EcoliWiki:b1713 , Mint:MINT-1231494 , ModBase:P07395 , Pride:P07395 , Protein Model Portal:P07395 , RefSeq:NP_416228 , SMR:P07395 , String:511145.b1713 , UniProt:P07395

Relationship Links: InterPro:IN-FAMILY:IPR002547 , InterPro:IN-FAMILY:IPR004532 , InterPro:IN-FAMILY:IPR005121 , InterPro:IN-FAMILY:IPR005146 , InterPro:IN-FAMILY:IPR005147 , InterPro:IN-FAMILY:IPR009061 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR020825 , PDB:Structure:3PCO , Pfam:IN-FAMILY:PF01588 , Pfam:IN-FAMILY:PF03147 , Pfam:IN-FAMILY:PF03483 , Pfam:IN-FAMILY:PF03484 , Prosite:IN-FAMILY:PS50886 , Prosite:IN-FAMILY:PS51447 , Prosite:IN-FAMILY:PS51483 , Smart:IN-FAMILY:SM00873 , Smart:IN-FAMILY:SM00874 , Smart:IN-FAMILY:SM00896

Summary:
The β subunit of PheRS contains the Phe-tRNAPhe binding site [Lavrik82, Khodyreva85]. The editing site of the enzyme localizes to the B3/B4 domain of the β subunit [Roy04]. Amino acid residues involved in the editing activity have been identified [Ling07]. The B2 OB-fold domain is not essential for catalytic activity, but may play a role as a secondary tRNA binding site in post-transfer editing [Roy06].

Isolated β subunits exist primarily as monomers [Bobkova91].

Citations: [Comer76, Russell71]

Essentiality data for pheT knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

References

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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