MMSYN1 0163 cborstin

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Author Information

Catherine Borsting

Basic Information

  • ID: MMSYN1_0163
  • Name: alaRS
  • Organism: JCVI-Syn3.0
  • Description:This gene is responsible for Alanine--tRNA ligase, which is important for Transfer RNA. [1] RNA comes in three different forms, messenger RNA, transfer RNA, and ribosomal RNA. Transfer RNA (or tRNA) is responsible for desiphering the mRNA, which copies the genetic information from the DNA. [2]

This enzyme is involved in catatylizing the chemical reaction:

ATP + L-alanine + tRNAAla ← → AMP + diphosphate + L-alanyl-tRNAAla

Specifically, this catalyzes the attachment of alanine to tRNA. This occurs in a two-step reaction, first Ala-AMP is formed by the activation of alanine by ATP. Next, Ala-AMP is transferred to the accepter end of tRNA.[3]

  • DNA Length: 2688 base pairs.
  • DNA sequence:

ATG AAG AAA CTT TCA ACG AAC CAA ATT CGT AAG ATC TGG CTT GAC TTT TTT ATC TCA AAA AAT CAC TAC TTC TTA GAG ACA GTC AGC TTG ATC CCT GTCGAT GAC CCC AGT CTT CTT TGG ATT AAC TCT GGA GTT GCT ACG CTG AAG CCT TAC TTC GAT GGG CGC AAA ACA CCA CCT TCC CCA CGT CTT ACG AAT TCGCAA AAA GCC ATC CGT ACG AAT GAT ATC GAG AAT GTG GGC GTC ACG GCA CGT CAC CAT ACC ATG TTC GAG ATG CTT GGG AAC TTC TCT ATC GGC GAT TACTTT AAG AAG GAG GCG ATC GAA TTG GCC TGG GAG TTA CTT ACT GAC AAA AAT TAT TTT GAT ATC GAT AAA GAC AAG CTT TAC ATT ACA GTG TTT AAC GAAGAT ACA GAG GCC TAC AAT ATC TGG AAA GAC GTA ATC AAG ATT GAT GAG GAT CAT ATC TTT CGT CTG AGC CGT AAA ACA AAC TTT TGG GAC GTG GGG CAAGGG CCA TGT GGG CCG AAT ACG GAA ATC TTT TAC GAT CGT GGC GAG ATT TGG GAT CCG AAT AAA ATC GGC CCA CGC CTG ATT TCA GAC GAC ATC GAA AACGAT CGT TAT ATC GAA GTT TGG AAC ATC GTT TTT AGT CAG TTT AAT AAC GAC GGG AAC GAT AAC TAT ACG GAG CTG CCA CGT AAG AAC ATT GAC ACT GGCGCC GGT CTG GAG CGT TTT GCG TCC ATT TTT CAG AAT ACC CCG ACT AAC TTT GAA ACA GAT ATT TTC TAT CCA ACT ATC AAA AAG GTC GAA CAA TTG ACTAAC GAC CAG TTC AAG TAC TCT ATT GAT AAT TAC TTT AAT CCC AAT AAA AAA CAA ACC CGC ATT AAT ACT GCG TTT AAA GTT ATC GCC GAT CAT ATC CGTGCC ACA GTT TTC GCA ATC TCG GAC GGC GTT TTT CCT GGT AAT AAG GAC CGC GGT TAT ATT ATT CGC CGC CTG ATC CGC CGT TCA TGC GTA TTC GGT AAAGAA TTA GGG ATT AAG CAA GCC TTC CTG TAC AAG TTA GTA GAT AGC GTC ATC GAG TCG ATG AAA GAA TTC TAC CCG TAC TTG ATC GAC AAG AAA ACA CTTGTT GAG CAG ACA ATC AAG GAC GAG GAG GAA AAA TTC CTT AAG ACC TTA TCC AAA GGG TAT GAT TTG CTG GAA AAC ATT ATC AAG ACT AAG AAC ACT GTAAGT GAC AAA GAC GCA TTA CTG TTA TTT GAG TCC TAT GGA TTT CCC ATT GAA CAA ACA ATC GAA ATC AGT GAG CTG AGT AAC GTG ACA GTG GAC ATT GAGGGC TTT AAA AAA CTT CTG GAG CAA ACA AAG CAG GCC ACA CGT AAT GCG CGT AAA GAC TTA AAG GCC TGG GAC AAA CAA AAC GAG CTG TTC ACG AAG TTGAAG GTT GAA TCA GAA TTC ACT GGG TGG TCA GAA ACT TCA CGC GAC AAT GCG AAA GTG ATC TAC ATG TTC ACG GAT CAA AAA CAG GTA GAG TCA ATT ACCGAC CAG GAA GCA TTC GTG ATC TTA GAT AAA ACA CCC TTT TAC GCC GAA AAA GGC GGT CAG GCG GCA GAC TCT GGG ATC ATC TTT AAT GAT CAG ATG AAGGGT TTC GTA ATC GAC GTT CAG CAG GGT CCA ATG CAC CAA AAC ATC CAC CGC ATC AAG GTG CAG GGG ACC TTG AAG GTA AAT GAC CTG GTC AAC TGT CGTGTG GAT GAA GAG AAG CGC ATC TAT ACT ATG AAG AAT CAC TCG GGG ACA CAT ATG ATT CAC TAC GCA TTA CGT GAA GTA CTG GGT ACG TCG GTA ATG CAGTCC GGT AGC TAC AAC GAT GAA AAT GGG TTA CGC ATG GAC TTC ACT TAT CAC CGT CTG CCC ACC AAC CAA GAG TTA CTG AAG GCC CAG AAT TTA GTA TTGGAG AAA ATC AAG AAC AAA ATT GAC CGT CAG ACC TAT TTC TGT TCG TTA GAA GAG TCA GTC AAA AAG CAC CAA GCC CTG GCG TTC TTT ACT GAG AAG TATGAT GAG ATC GTA CGC GTC ATC AAA TTT GGT GAC TTT TCA TCT GAG TTA TGT GGC GGT ACA CAT GTG AAT AAC ACA TCG GAA ATT GAA GAC TTT ATT ATTACA GGC ATC GAG TCA AAG GGG TCT GGA TTA TAT CGT ATT AAA TGC TTA ACT AGC TTT AAG ACA GTA AAC GAG TAC CTG AAC GAG CAA TTC AAA ATT TACAAA GAC CAA GCG GAG ATC ATT ATT GAT AAG TAC AAC CAG AAC AAA GAC TTG TTG AAG AAT GAC CAG CTT GAG AAT ATC TAT TTG CAG ATT AAG AAC ATTACG ATT AAT AAG GAT AAT TTG TTA GTT ATC AAA GAC TTA TTA GAC AAA CTT AAA GAA ATC AAC AAG GAC TAC GAC AAA AAG GTG AAC GAC CTT ATT ACGGCG AAT AAA TTG CTT AAA TAC AAA GAT TTA ACG CCA AGC TTA AAT AAG GAC AAC ATT AAT GAG ATC CGC TTA GAG ACC ACC GAC TTG AAT ATT AAG GATTTA AAA CAG TTA GCC GAT GAC CTG CGT AAC AAG TAT GAC GAC CTG ATT GTT ATC TTG CTT TCA TCT ACG AGT GAG AAT AAT TTT GTG GTC GTT GCG GTCAGT CAA AGC TTA CAG AAC AAA TAT AAA GCG ATC GAC ATT TTC AAT AAC CTT GAA GGC TAC GAA ACT AAG GGG GGG GGG AAT GCC AAT CTG GCG CAA GGTAAG TTT GTA AAG AAG

  • Amino Acid length: 896 amino acids.
  • Amino Acid sequence:

MKKLSTNQIRKIWLDFFISKNHYFLETVSLIPVDDPSLLWINSGVATLKPYFDGRKTPPSPRLTNSQKAIRTNDIENVGVTARHHTMFEMLGNFSIGDYFKKEAIELAWELLTDKNYFDIDKDKLYITVFNEDTEAYNIWKDVIKIDEDHIFRLSRKTNFWDVGQGPCGPNTEIFYDRGEIWDPNKIGPRLISDDIENDRYIEVWNIVFSQFNNDGNDNYTELPRKNIDTGAGLERFASIFQNTPTNFETDIFYPTIKKVEQLTNDQFKYSIDNYFNPNKKQTRINTAFKVIADHIRATVFAISDGVFPGNKDRGYIIRRLIRRSCVFGKELGIKQAFLYKLVDSVIESMKEFYPYLIDKKTLVEQTIKDEEEKFLKTLSKGYDLLENIIKTKNTVSDKDALLLFESYGFPIEQTIEISELSNVTVDIEGFKKLLEQTKQATRNARKDLKAWDKQNELFTKLKVESEFTGWSETSRDNAKVIYMFTDQKQVESITDQEAFVILDKTPFYAEKGGQAADSGIIFNDQMKGFVIDVQQGPMHQNIHRIKVQGTLKVNDLVNCRVDEEKRIYTMKNHSGTHMIHYALREVLGTSVMQSGSYNDENGLRMDFTYHRLPTNQELLKAQNLVLEKIKNKIDRQTYFCSLEESVKKHQALAFFTEKYDEIVRVIKFGDFSSELCGGTHVNNTSEIEDFIITGIESKGSGLYRIKCLTSFKTVNEYLNEQFKIYKDQAEIIIDKYNQNKDLLKNDQLENIYLQIKNITINKDNLLVIKDLLDKLKEINKDYDKKVNDLITANKLLKYKDLTPSLNKDNINEIRLETTDLNIKDLKQLADDLRNKYDDLIVILLSSTSENNFVVVAVSQSLQNKYKAIDIFNNLEGYETKGGGNANLAQGKFVKK

Function and Homologs

  • Product: Alanine--tRNA ligase
  • Module: ATP binding
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • alanine--tRNA ligase [Escherichia coli], 563 / 98% / 0.0 / 36%, link Accession
    • alanine--tRNA ligase [Escherichia coli], 562 / 98% / 0.0 / 36%t, link Accession
    • alanine--tRNA ligase [Escherichia coli], 559 / 98% / 0.0 / 36%, link Accession
  • Equivalent E. coli / JCVI functional protein: EG10034.

Expression

  • Expression Level: Low.
  • Expression Level Hypothesis: This is an important component in the attachment of Alanine to tRNA, and it would be expected that it would have higher levels of expression. In the counter organism, E.Coli, the level of expression is high, so this may be in error in the particular database that it was gathered from, given that this was a simulation.
  • Expression Level References and Description: This level was taken directly from the database for the simulated proteomic expression for Mycoplasma gentialium. Note, in the database it is referred to as: alanyl-tRNA synthetase, another common name for this gene. [1]
  • Expression Time: Early
  • Expression Time Hypothesis: This protein is crucial for translation, specifically in the creation of tRNA, so it must be expressed early.
  • Expression Time References and Description: Information was gathered mainly from previous sources, see description.

Gene Context

  • Other Components in the functional module: serS, MMSYN1_0061, catalyzes the attachment of serine to tRNA [2]
  • Possible Dependencies: MMSYN1_0792 atpA, produces ATP from ADP, ATP is necessary for the reaction this catalyzes to take place. [3]
  • Process: catalyzes the attachment of alanine to tRNA(Ala)
    • Input: ATP, L-alanine, tRNA(Ala)
    • Output: AMP, diphosphate, L-alanyl-tRNA(Ala)
    • Resource: Uniprot

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

References

Template:Reflist
  1. European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. "Alanine--tRNA Ligase." AlaS - Alanine--tRNA Ligase - Mycoplasma Mycoides Subsp. Mycoides SC (strain PG1) - AlaS Gene & Protein. N.p., 15 Feb. 2017. Web. 16 May 2017.
  2. Lodish, Harvey. "The Three Roles of RNA in Protein Synthesis." Molecular Cell Biology. 4th Edition. U.S. National Library of Medicine, 01 Jan. 1970. Web. 16 May 2017.
  3. "Alanine—tRNA Ligase." Wikipedia. Wikipedia Foundation, n.d. Web. 12 May 2017.