MMSYN1 0613

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Author Information

Catherine Lee

Basic Information

  • ID: MMSYN1_0613
  • Name: tyrS
  • Organism: JCVI-Syn3.0
  • Description: tyrS gene codes protein TyrRS. TyrRS 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. TyrRS belongs to the Class IC aminoacyl tRNA synthetases. TyrRS catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). It is located in the cytoplasm and functions in protein biosynthesis.
  • DNA Length: 1245 base pairs (incl. stop codon)
  • DNA sequence:

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

  • Amino Acid length: 414 amino acids
  • Amino Acid sequence:

MKNNILEELKWRGLIKQITNESKILDAQNNSDAVYCGFDPTADSLHVGHLMMIITLKRFADYNFKPIALIGGATGMIGDPSFKANERVLQTKDQVEHNINKISAQLKQIIPNVNFVNNNTWLSSISLIDFLRDIGKHFNLSYLLAKESIATRIQTGLSVTEFCYTMLQAYDFYYLYKNNNCSIQIGGSDQWGNITSGIDFISDTINKNNKAAGLTINLLTKSDGQKFGKTESGAVWLDKTKTSEYEFYQFWFNQTDQDSINLLKCLTFLTKEQIDNLIKEHQNQPSKHLLQKALASEMTKFVHQQQGLDKALKLTEAFFSGDLFSLTDDLFKMALNSLPNTQINKDTKVIDALIEVKAASSKREAREFLTNKAIMINNQIIEDENTLISSFDLIQNKYLLVKKGKKKYFVILIK

Function and Homologs

  • Product: tyrosine—tRNA ligase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • tyrosine--tRNA ligase [Mycoplasma leachii], 782 / 100% / 0.0 / 92%, WP_013447928.1
    • tyrosine--tRNA ligase [Mycoplasma feriruminatoris], 776 / 100% / 0.0 / 90%, WP_008364150.1
    • tyrosine--tRNA ligase [Mycoplasma capricolum], 775 / 100% / 0.0 / 90%, WP_011387503.1
  • Equivalent E. coli / JCVI functional protein: EG11043.

Expression

  • Expression Level: Low
  • Expression Level Hypothesis: Tyrosine only accounts for ~3% of amino acids in E. coli genes [1]. M. genitalium is much smaller than E. coli in terms of genome length, so the expression level here is Low instead.
  • Expression Level References and Description: M. genitalium model data, File:MgenitaliumSimProteinCounts.xlsx.
  • Expression Time: Early
  • Expression Level Hypothesis: tyrRS is involved in protein synthesis in translation, which occurs after transcription. So we would want the gene to be expressed early.
  • Expression Time References and Description: Research description above.

Gene Context

  • Other Components: TyrB, TyrB is the primary enzyme contributing to the synthesis of tyrosine. [2] (NOTE: TyrB not in database).
  • Possible Dependencies: Transamination, conversion of a ketoacid to the aminoacid. Required for the third step of the pathway. [3]
  • Process: L-tyrosine biosynthesis
    • Inputs: chorismate, NAD+, L-glutamate
    • Outputs: NADH, CO2, 2-exoglutarate, L-tyrosine
    • Reference: EcoCyc [4]

Construct

We will do this - not part of your assignment.

  • 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