MMSYN1 0537

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Author Information

Marissa MacAvoy

Basic Information

  • ID: MMSYN1_0537
  • Name: pyrH_bact: UMP kinase
  • Organism: Mycoplasma mycoides JCVI-Syn3.0
  • UniProt ID: Mycoplasma mycoides entry F4MQB3
  • Description: UMP kinase [1] is an enzyme that catalyzes the reaction that turns Adenosine triphosphate, ATP, [2] and Uridine monophosphate, UMP, [3] into Adenosine Diphosphate, ADP, [4] and Uridine diphosphate, UDP. This is an important reaction in cells because ATP is involved in cellular respiration and the regulation of it is crucial. Additionally, the synthesis of UDP is critical because UDP is the starting point of the synthesis of pyrimidine nucleotides, Thymine (T) and Cytosine (C) [5]. These are half of the base pairs that make up DNA, so it important for UMP kinase to catalyze this reaction and eventually aid in the production of essential nucleotides. Without UMP kinase to speed up the reaction of ATP and UMP to ADP and UDP could not be replicated.
  • DNA Length: 711 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 237 amino acids.
  • Amino Acid sequence:

MNYKYKTVLLKLSGEALKGDAEVYDKKCLDNIASQIVHLAKNGLKLAIVIGGGNIWRGKLGENIGMDAINADYMGMLATVMNGLALESTITKMGYDKIKVYSSLPIKTVTDDYNFKKARIKMNEGFISIFVGGTGYSYFTTDTNATIRAIEIGADVILMAKNGVKGVYDKDPKQHSDAKFIKRLTHQEVVDKQLRIMDLTAATLAKDANLKIEVFDMSGDNNIIKVLENKLESTIIE

Function and Homologs

  • Product: Uridylate kinase
  • Closest homologous proteins:
    • UMP kinase [Mycoplasma feriruminatoris], Max score: 459, Query Cover: 100%, E-Value:0.0, Ident: 96%, Accession
    • UMP kinase [Mycoplasma leachii], Max score: 458, Query Cover: 100%, E-Value:0.0, Ident: 95%, Accession
    • UMP kinase [Mycoplasma capricolum], Max score: 458, Query Cover: 100%, E-Value:0.0, Ident: 95%, Accession
  • Equivalent E. coli / JCVI functional protein: EG11539.

Expression

  • Expression Level: Medium, 12 Proteins/cell
  • Expression Level Hypothesis: It makes sense that the Uridylate Kinase gene would be expressed to a medium level because the gene does play a crucial role in the cell, but does not need to be created constantly. UMP kinase is essential as a catalyst for the reaction that turns ATP and UMP into ADP and UDP. Furthermore, this reaction leads to the synthesis of half of the nucleotides, so it is critical that the cells have enough of the gene in the cell. That being said, this enzyme is a catalyst and does not get used up during the reaction, so the cells only need a medium amount of the gene instead of a high expression level.
  • Expression Level References and Description: Data for the expression level was gathered from the M. genitalium database [6]. The exact gene was listed in the database.
  • Expression Time: Early
  • Expression Level Hypothesis: Based on the function of the UMP kinase gene, the gene should be expressed early because the gene is involved in the reaction that makes nucleotides. It is crucial to have nucleotides in order to create mRNA and additional proteins, so UMP kinase should be expressed earlier.
  • Expression Time References and Description: The expression time was deduced from the function of the gene. Because UMP kinase is a transferase enzyme, it is important to have expressed early on. [7].

Gene Context

  • Other Components: No other components
  • Possible Dependencies: Because this protein is a catalyst, it requires the chemicals to be present; therefore, the protein is dependent on adenosine triphosphate and uridine monophosphate synthesis.
  • Process: Catalyst to the reaction that turns ATP and UMP into ADP and UDP
    • Inputs: ATP, UMP
    • Outputs: ADP, UDP

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file