MMSYN1 0535

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Author Information

Feddi Roth

Basic Information

  • ID: MMSYN1_0535
  • Name: argS
  • Organism: JCVI-Syn3.0
  • Description: Arginine-tRNA ligase is an aminoacyl tRNA synthase [1] . It links amino acids convalently to their specific tRNA molecules through ATP hydrolysis [2] . Ligases are enzymes that calatyze the linking of two molecules through a chemical bond using hydrolysis, in this case of ATP [3]. ATP hydrolysis is where energy is release through breaking one of the phosphate bonds in ATP, converting it to AMP + P [4]. Synthases are enzymes that catalyze reactions involving the linking of two molecules, in this case linking the Arginine amino acid to its tRNA [5]. The specific reaction is ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) [6].
  • DNA Length: 1662 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 554 amino acids.
  • Amino Acid sequence:

MSTTIIEMFYNDLKNICQKLNITKEPIIEINKNNTPGLLSSSICLISSKQVNKKPLELAEIFKQELLLTNSYLNIDIAAPGFLNVLVKPEILSNVISNVLSLKSKYGNLEKQNKTINIEYVSANPTGYLHVGHARNAVIGSVLVNLFKKAGYNVQTEYYVNDAGNQINVLAVTVFVHYLQALNIDAKKPENCYAGDMYEDLAKIIINKYNDQFKDIKYTDNKILDDNVHSLFKQISIDYFLKIIKQQLADFNVKIKHWSSEQEVYDTHQIEKVLKLYESKDALYYKDDALFLKTTQFGDDKDRVLVKSDKTYTYILPDLATHNLRIKRTKADKLINVWGGDHHGYIKRMQAGLALLGNDPDILEIQMVQMVRLIKDGSEYKMSKRKGTAVWLVDILELVGVDALRYMLASKSSNSHMDLDLDLITLKNSSNPVYYAQYATARCHSILNQAKTKKITPLIKQTNLLNNPKEIELLLILDNFKEVIKNSANNRSTQQICDYIQNICKIFHSYYAEIKIIDENDLQLTKLRLGFIKAILQVLKNAFFIIGIQPVVEM

Function and Homologs

  • Product: Arginine-tRNA ligase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • arginine--tRNA ligase [Mycoplasma mycoides], 1105/100%/0.0/98%, WP_011166776.1
    • arginine--tRNA ligase [Mycoplasma capricolum], 1035/100%/0.0/94%, WP_036430857.1
    • arginine--tRNA ligase [Mycoplasma leachii], 1032/100%/0.0/94%, WP_013447694.1
  • Equivalent E. coli / JCVI functional protein: EG10071.

Expression

  • Expression Level: medium
    • Expression Level Hypothesis: I hypothesize that because tRNA molecules and the amino acids they carry are essential to creating other proteins the cell needs, there would need to be a substantial amount of Arginine-tRNA ligase in the cell. However, since they can be reused only medium level expression is needed.
    • Expression Level References and Description: Expression level was found using the information about argS protein found in the whole cell model Mycoplasma genitalium created by a group at Stanford using File:MgenitaliumSimProteinCounts.xlsx.
  • Expression Time: Right at the beginning.
    • Expression Time Hypothesis: I hypothesize that because tRNA molecules and the amino acids they carry are essential to creating other proteins the cell needs, the argS protein would be needed right away to ligate arginine to its tRNA and thus allow the amino acid arginine to be used to create important proteins for the cell.
    • Expression Time References and Description: The expression time was inferred (see hypothesis above) but no resources were found and thus I am unsure of my choice of expression time.

Gene Context

  • Other Components: This module has only one component.
  • Possible Dependencies: Arginine biosynthesis.
  • Process: arginyl-tRNA aminoacylation [7]
    • Inputs: ATP, L-arginine, tRNA(Arg)
    • Outputs: AMP, diphosphate, L-arginyl-tRNA(Arg)

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
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10071
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10071
  • https://en.wikipedia.org/wiki/Ligase
  • https://en.wikipedia.org/wiki/ATP_hydrolysis
  • https://en.oxforddictionaries.com/definition/synthase
  • http://www.uniprot.org/uniprot/A0A014MG93
  • http://www.uniprot.org/uniprot/A0A014MG93
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