MMSYN1 0198

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Author Information

Catherine Borsting

Basic Information

  • ID: MMSYN1_0198
  • Name: rplT
  • Organism: JCVI-Syn3.0
  • Description: This gene is an important component for ribosomes, a type of RNA, in translation. RNA comes in three different forms, messenger RNA, transfer RNA, and ribosomal RNA. Messenger RNA (or mRNA) copies the genetic information from the DNA. Transfer RNA (or tRNA) is responsible for desiphering the mRNA. Ribosomal RNA (or rRNA) uses a set of proteins to form ribosomes. [1] Ribosomes catalyzes mRNA protein synthasis. To allow tRNA bindings, the ribosomes expose the codons of mRNA. ⅓ of the mass of the ribosome consists of protein (broken down into smaller subunits), the other is made up of RNA. [2] The protein L20 is responsible for binding directly to 23S ribosomal RNA and is necessary for first step in the in vitro assembly of the 50S ribosomal subunit, but not for its protein synthesizing functions. [3] This 50S ribsomal mainly consists of other proteins, but also contains ribosomal RNA. [4]
  • DNA Length: 357 base pairs.
  • DNA sequence:

ATG GCG CGC GTT AAG TAC GGA AAA GTC ACT CGT GCC CGT CGT AAA CGC TGG ATT AAA TTG GCG AAA GGA TAT TTC GGG ACA AAA AAA TCC TCT TAT AAGAAG GCA CAT GAA CAA GTC ATC CGT TCT ATG GCC TAC GCC TTC ATT GGT CGC AAG GAG CGT AAG CGT GAT TTC CGC TCA CTT TGG ATT GTG CGT ATC AACGCC GCC GTG CGT CCC GAA GGA TTA AGC TAT TCA ACC TTT ATG CAC GGT CTG AAG TTA GCG AAC ATT AAT ATC AAC CGC AAA ATG CTG TCA GAA CTT GCAATT AAT AAT TCG GAA GAA TTT AAG CAG ATC GTT CAA CAG GCA AAA AAG GCC CTG AAC AAA

  • Amino Acid length: 145 amino acids
  • Amino Acid sequence:

MARVKYGKVTRARRKRWIKLAKGYFGTKKSSYKKAHEQVIRSMAYAFIGRKERKRDFRSLWIVRINAAVRPEGLSYSTFMHGLKLANININRKMLSELAINNSEEFKQIVQQAKKALNK

Function and Homologs

  • Product: ribosomal protein L20
  • Module: Ribosome
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • LSU ribosomal protein L20p [Escherichia coli ISC11], 115 / 98%/1e-32/49%,Link Accession
    • Chain O, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome, 103 / 95% / 3e-28 / 44%, Link Accession
    • 50S ribosomal protein L20 [Escherichia coli], 101 / 98% / 2e-27 / 49%, Link Accession
  • Equivalent E. coli / JCVI functional protein: EG10881

Expression

  • Expression Level: High.
  • Expression Level Hypothesis: This gene encodes for a protein that is crucial for the in vitro assembly process of the 50S ribosomal subunit, a component of the ribosome. Naturally, because ribosomes are a crucial component of translation, necessary for cell growth and function, the level would be high.
  • Expression Level References and Description: This level was taken directly from the database for the simulated proteomic expression for Mycoplasma gentialium [1]
  • Expression Time: Early
  • Expression Time Hypothesis: This protein is crucial for a ribosomal subunit, and thus crucial for the translation process, so it must be expressed early.
  • Expression Time References and Description: Information was gathered mainly from previous sources, see description.

Gene Context

  • Other Components: MMSYN1_0666 rplV (50S ribosomal protein L22), binds to 23S rNA, important for the assembly of 50S, catalyzed by rplT [2]
  • Possible Dependencies: MMSYN1 0645, rpoA, catalyzes the transcription of DNA into RNA, required for translation to take place and thus the ribosome [3]
  • Process: catalyzes the peptidyl transfer reaction
    • Input: aminoacyl-tRNA, carbonyl group of a peptidyl-tRNA
    • Output: peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site, deacylated tRNA in the P site
    • Resources: Wikipedia

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. 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.
  2. EMBL-EBI, InterPro. "InterPro." Ribosomal Protein L20 (IPR005813). N.p., n.d. Web. 16 May 2017.
  3. European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. "50S Ribosomal Protein L20." RplT - 50S Ribosomal Protein L20 - Mycoplasma Mycoides Subsp. Mycoides SC (strain PG1) - RplT
  4. "50S." Wikipedia. Wikimedia Foundation, 16 Apr. 2017. Web. 16 May 2017.