MMSYN1 0447 EPinilla

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Author Information

Emanuel Pinilla

Basic Information

  • ID: MMSYN1_0447
  • Name: dUTP diphosphatase
  • Organism: JCVI-Syn3.0
  • Description: Catalyzes the hydrolysis of nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates (dUTP, dTTP and dCTP).

Catalysis of the reactions:

dUTP + H2O = dUMP + diphosphate.

dTTP + H2O = dTMP + diphosphate.

dCTP + H2O = dCMP + diphosphate.

The nudI gene product is a member of the Nudix hydrolase superfamily of nucleoside diphosphatases. The preferred substrate of the purified enzyme is dUTP, but it also shows 67 and 58% of activity with dTTP and dCTP, respectively. The enzyme is a monomer in solution. [1]

  • DNA Length: 504 Base Pairs (Includes Stop Codon)
  • DNA sequence:

ATG ATC GAT AAT AAG ACG TTG AAA TGG TTG AGC GAA AAA CAA ATC ATT CTG GAC CAA TTT ATC CAA AAC AAG TGG AAT TTT AAA AAC GAC AAA ACG CTT CTG GAC AAG AAA TTA ACC GCA TTT TTA GTT GAG CTT GGT GAG TAT GCA AAT GAA GAA CGC TCA TTT AAG TAT TGG TCG AAC AAA AAG CCG TCA GAT CTT GAG ATT CAA TTG GAT GAG TAC ATT GAT GGA ATC CAT TTC ATT ATC TCC GTT GGT AAT CAG ATT AAC TAC AAC TTT TTG GAG TTC AAC TAC AAC TTC TTG AAT AAG GAG TCG ATC ATT GAC ATC TAC TTT GAA ATT ATT TCT TGC CTT AAC AGC TTC ATC AAG GAG AAC AAC AAC ACG AAT TAC TCT AAT TTG TTG AAT GCT TTC TTA AAT ATC TGC GAG ATC AAG AAC TAT ACT CAG GAT CAA ATC ATC AAT GCC TAT AAT ATC AAA AAT GAG ATC AAT TTC CAA CGT CAA AAT AAT AAC TAT TAA

  • Amino Acid length: 167 Amino Acids
  • Amino Acid sequence:

MIDNKTLKWLSEKQIILDQFIQNKWNFKNDKTLLDKKLTAFLVELGEYANEERSFKYWSNKKPSDLEIQLDEYIDGIHFIISVGNQINYNFLEFNYNFLNKESIIDIYFEIISCLNSFIKENNNTNY SNLLNAFLNICEIKNYTQDQIINAYNIKNEINFQRQNNNY*

Function and Homologs

  • Product: DUTP diphosphatase
  • Module: Nucleotide Specific Salvaging
  • Closest homologous proteins:

dUTPase superfamily [Mycoplasma mycoides] 324 / 100% / 5e-112 / 100%, WP_020862760.1

dUTP diphosphatase [Mycoplasma capricolum] 306 / 100% / 3e-105 / 93%, WP_036431823.1

dUTP diphosphatase [Mycoplasma leachii] 305 / 100% / 2e-104 / 93%, WP_013447767.1

UniProt ID: P52006

Expression

  • Expression Level: High (not on the excel sheet)
  • Expression Level Hypothesis: Expression is high because the gene function is to hydrolyze nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates. This function is very important and because of this the expression level must be high as this is an ongoing process in the cell and high expression is necessary. The functional category is nucleotide salvaging and this also hints towards high expression being required.
  • Expression Level References and Description: The gene's expression was not located on either M. genitalium model data nor the E. coli proteome. The expression level is induced due to the function of the gene.
  • Expression Time: Early
  • Expression Level Hypothesis: This gene is expressed early because its purpose is to recover bases and nucleosides that are formed during degradation of RNA and DNA. This gene's role in nucleotide salvaging means it is very important for the process of replication and protein synthesis. Since the gene corrects nucleotides it is crucial that it is present in the cell and expressed at an early time to assure that everything synthesized for the cell or any replication is done without faulty DNA and this also helps to prevent mutations. Due to gene function and importance, the expression time must be early.
  • Expression Time References and Description: The expression time was gathered due to the function of the gene and from that it is evident that the expression time is early. Research description above.

Gene Context

  • Other Components: Its goal is to break down dUTP and does not require other proteins in the complex to do its function. It does not directly interact with other components. (looked on EcoCyc and uniProt and there were no other components found)
  • Possible Dependencies: A pH of 8.5 is optimal. Mg+2 is a cofactor and serves as a ligand. dUTP must be made in the first place for the process to get underway. Nucleotide biosynthesis or DNA replication need to happen before nucleotides are broken down
  • Process: Nucleotide Salvaging
    • Inputs: dNTP (N may be U,T or C although mainly U), H2O, degradation intermediates

Could also be dNMP (N may be U,T or C although mainly U), diphosphate as this is a reversible mechanism.

    • Outputs: dNMP (N may be U,T or C although mainly U), diphosphate.

Could also be dNTP (N may be U,T or C although mainly U), H2O, degradation intermediates as this is a reversible mechanism.

  • Reference: EcoCyc dUTP diphosphatase activity

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
  • UniProt, UniProt
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