MMSYN1 0529

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Author Information

Blake Salvador

Basic Information

  • ID: MMSYN1_0529
  • Name: pheRS; pheS (Phenylalanine-tRNA ligase alpha subunit)
  • Organism: JCVI-Syn3.0
  • Description:

This protein is a subunit of Phenylalanine-tRNA ligase. It is involved in ATP binding and nucleotide binding [1]. The purpose of the complete enzyme is to catalyze the formation of a phenylalanine-tRNA complex: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe) [2].

The ligase is a member of the aaRS(Aminoacyl-tRNA synthetase) family of proteins, enzymes which catalyze the formation of an ester linkage between tRNA and the appropriate amino acid [3].

  • DNA Length: 1053 base pairs.
  • DNA sequence:

ATG ATC GAG CAA TTG AAC GAG ATC CTT AAT AAC TTT AAG GTT AAA TTA GAG CTG GTC AAA GAT CTT AAT TCG TGG GAA GAG CTG AAA AAG GAG TTC ATC GGA AAA GAC TCA AGT CTT ACC ACC ATC CTG AAG TCA ATT AAG ACA ATC TCA TCC GAT AAG AAA CAG GAG ATT GGC AAA CTG GCT AAT CAG ATT CGC GTC GAG ATT ATT AAC CAA TTA AAC GAA AAA CAA GAG CAA CTT AAA AAT AAG GAA CTT TTG GTG AAA TTA GAA AAA GAG AAA ATT GAC GTT ACG TTA ACC AAC TCC TCA TTA AAG TTT GGT AGT AAA CAT GTA TTG AAC ATC GTT ATT GAA GAA ATT TCA GAT ATT TTC ACG GAG ATC GGG TTC GAG ATG GTG AGC GGT ACT GAA ATC GAG TCG GAT CTT TAC AAC TTC CAA AAA TTA AAC CTG CCC GTA GAT CAT CCG GCT CGT GAT ATG CAG GAT ACT TTC TAC TTG GAT AAC AAT CTG GTT TTA CGT ACT CAT TGT ACG AAT ATG ACT TCC CGC ATG TTG ACA AAG CTG GCA TCT CTT AAG ACA GAA GAT AAT AAT TTA GCC GTA ATT TCA TAT GGT AAC GTA TAC CGC CGC GAC GAT GAC GAC GCC ACG CAC AGC CAT CAG TTC ATG CAA ATC GAT GGC TTC GTC GTT GGC AAC AAA ATT AGC TTC GCT AAC TTG AAG TGG ATC CTG AAG TAC ATG TGC CAG CGT TTG TTC AAT AAA GAC ATT AAC ATT CGT TTG CGT CCT TCT TAT TTT CCT TTT ACT GAA CCA TCC GTT GAA GTG GAT GTA AGT TGT TTC AAG TGC GAT TCT AAG GGC TGT TTT ATC TGC AAA AAG ACT GGC TGG ATC GAA ATT TTA GGG GCC GGA ATG ATT AAT GAG CAT GTT CTT AAA CTT AAT GGG TTA GAC CCT ACT AAG TGC TCG GGA CTG GCC TTT GGG ATC GGT ATT GAG CGC ATC GCC ATG CTT AAG TTT AAC ATC TCC AAT ATC CGC AAC TTC TAT GAG AAT AAC GTT AAA TTC CTT GAA CAG TTT AAA TTT TAC AGT GAG TGA

  • Amino Acid length: 350 amino acids.
  • Amino Acid sequence:

MIEQLNEILNNFKVKLELVKDLNSWEELKKEFIGKDSSLTTILKSIKTISSDKKQEIGKLANQIRVEIINQLNEKQEQLKNKELLVKLEKEKIDVTLTNSSLKFGSKHVLNIVIEEISDIFTEIGFEMVSGTEIESDLYNFQKLNLPVDHPARDMQDTFYLDNNLVLRTHCTNMTSRMLTKLASLKTEDNNLAVISYGNVYRRDDDDATHSHQFMQIDGFVVGNKISFANLKWILKYMCQRLFNKDINIRLRPSYFPFTEPSVEVDVSCFKCDSKGCFICKKTGWIEILGAGMINEHVLKLNGLDPTKCSGLAFGIGIERIAMLKFNISNIRNFYENNVKFLEQFKFYSE

Function and Homologs

  • Product: Phenylalanine-tRNA ligase alpha subunit
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Phenylalanine-tRNA ligase alpha subunit (Mycoplasma capricolum), 682/100%/0.0/95%, [WP_036431702.1]
    • Phenylalanine-tRNA ligase alpha subunit (Mycoplasma feriruminatoris), 672/100%/0.0/93%, [WP_008362869.1]
    • Phenylalanine-tRNA ligase alpha subunit (Mycoplasma leachii), 669/100%/0.0/93%, [WP_013447697.1]
  • Equivalent E. coli functional protein: EG10709.

Expression

  • Expression Level: Medium.
  • Expression Time: Early.
    • Expression Time References and Description: Where did you gather the expression time information from?

Expression

  • Expression Level: Medium.
  • Expression Level Hypothesis: The pheS protein catalyzes binding phenylalanine to the appropriate tRNA molecule. This process is essential for translation to proceed smoothly and must occur constantly in the cell, which is why it cannot have a "low" expression level. However, phenylalanine is only one of twenty essential amino acids, so it does not necessarily need a "high" expression level (and thus medium is appropriate).
  • Expression Level References and Description: Gathered from Mycoplasma genitalium simulation of protein expression by Karr et. al: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: Early.
  • Expression Level Hypothesis: The function of the gene means that the cell must begin expression of this protein early on in its life, or else it cannot produce proteins (as they will lack phenylalanine). Its medium expression level implies that the cell will probably not deplete its supply of pheS immediately, and so it does not need expression of this protein right at the beginning. However, it will definitely begin expressing this protein early on.
  • Expression Time References and Description: The expression level gave me a decent grasp on the expression time, so see above. Also, this book excerpt gave me a deep understanding of how the protein works, giving me an idea of its possible expression time: [[4]].

Gene Context

  • Other Components: MMSYN1_0528 --> The beta subunit of phenylalanine-tRNA ligase.
  • Possible Dependencies: MMSYN1_0645 --> RNA polymerase subunit alpha (rpoA) is necessary for RNA transcription. This, in turn, is necessary for tRNA production, which must occur for phenylalanine to be bound to its appropriate tRNA.
  • Process: Ligation of phenyalanine to tRNA
    • Inputs: ATP, L-phenylalanine, tRNA(Phe)
    • Outputs: AMP, diphosphate, L-phenylalanyl-tRNA(Phe)

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file