MMSYN1 0773

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Author Information

Marissa MacAvoy

Basic Information

  • ID: MMSYN1_0773
  • Name: nrdF
  • Organism: Mycoplasma mycoides JCVI-Syn3.0
  • UniProt ID: Mycoplasma mycoides Entry F4MQY0
  • Description: The nrdF gene in Mycoplasma mycoides helps to salvage nucleotides during the process of protein degredation which helps organisms produce more complicated molecules if they do not undergo de novo synthesis. [1] This process is essential in organisms in order to produce all of the complex molecules that organisms need to survive. UniProt also suggests that this gene may aid in oxidation/reduction reactions which are critical chemical reactions involving the exchange of protons. These chemical Redox reactions are important on a biological level in many reactions including cellular respiration. [2] A final possible function of this gene is in aiding deoxyribonucleotide biosynthetic processes [3].
  • DNA Length: 1,017 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 339 amino acids.
  • Amino Acid sequence:

MAKEQKYYHESVSPIEFVKNNFKGNLRSVNWNVINDEKDLEVWNRITQNFWLPEKIPVSNDLSSWRSLSSEWQQLVTRTFTGLTLLDTVQATVGDVAQIEHSLTDHEQVIYSNFAFMVGVHARSYGTIFSTLCSSEQIEEAHEWVVKTETLQKRAKALIPYYTGTDPLKSKVAAALMPGFLLYGGFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQKKVAKLPVEKQAEMKEFVFKLLYELIDLETAYLKELYAGFDIVDDAIRFSVYNAGKFLQNLGYDSPFSEEETRIEPEIFNQLSARADENHDFFSGNGSSYVMGVSVETEDEDWEF

Function and Homologs

  • Product: Ribonucleoside diphosphate reductase 2 betachain
  • Closest homologous proteins:
    • Ribonucleoside-diphosphate reductase [Mycoplasma capricolum], Max score: 683, Query Cover: 100%, E-Value: 0.0, Ident: 97%, Accession
    • Ribonucleoside-diphosphate reductase [Mycoplasma leachii], Max score: 682, Query Cover: 100%, E-Value: 0.0, Ident: 97%, Accession
    • Ribonucleoside-diphosphate reductase subunit beta [Mycoplasma feriruminatoris], Max score: 682, Query Cover: 100%, E-Value: 0.0, Ident: 97%, Accession
  • Equivalent E. coli / JCVI functional protein: EG12381.

Expression

  • Expression Level: Medium, 58 Proteins/cell
  • Expression Level Hypothesis: The nrdF gene is likely expressed to a medium level because it is used in essential processes like nucleotide salvaging. This gene is necessary for for cell to continue to make new molecules; however, the protein is not used up during any of these processes so it does not need an excess of the proteins in the cell.
  • Expression Level References and Description: Data for the expression level was gathered from the M. genitalium database [4]. The exact gene was listed in the database.
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Based on the fact that the nrdF gene is involved in the production of deoxyribonucleotides and oxidation reactions, the gene should be produced immediately in the cell so that other processes can take place.
  • Expression Time References and Description: Using the function of the nrdF gene, I deduced that the gene should be expressed immediately. Information on the function came from UniProt.

Gene Context

  • Other Components: Ribonucleoside-diphosphate reductase, alpha chain or nrdE
  • Possible Dependencies: The nrdF gene cannot function without the other subunits (like the alpha chain). As a collective, this protein requires nucleotides in order to function so the nrdF gene is dependent on nucleotide synthesis. [5]
  • Process: Deoxyribonucleotide biosynthetic process [6]:
    • Inputs: Deoxyribonucleoside, phosphate group
    • Outputs: Deoxyribonucleotide

Construct

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  • 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