EG13275 EPinilla

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Author Information

Emanuel Pinilla

Basic Information

  • ID: EG13275
  • Name: nudI
  • Organism: E.coli
  • 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.[1]

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.[2]

  • DNA Length: 426 Base Pairs (including STOP codon)
  • DNA sequence:

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

  • Amino Acid length: 141 Amino Acids
  • Amino Acid sequence:

MRQRTIVCPLIQNDGAYLLCKMADDRGVFPGQWAISGGGVEPGERIEEALRREIREELGEQLLLTEITPWTFSDDIRTKTYADGRKEEIYMIYLIFDCVSANREVKINEEFQDYAWVKPEDLVHYDLNVATRKTLRLKGLL*

Function and Homologs

  • Product: Nucleoside triphosphatase NudI
  • Module: Nucleotide Specific Salvaging
  • Closest homologous proteins:

Nucleoside triphosphatase NudI Escherichia coli O78:H11 (strain H10407 / ETEC) / 743 / 100% / 4e-98 / 100%, E3PDV3

Nucleoside triphosphatase nudI Achromobacter sp. / 743 / 100% / 4e-98 / 100%, A0A0M7NT22

Nucleoside triphosphatase NudI Shigella sp. PAMC 28760 / 743 / 100% / 4e-98 / 100%, A0A142H4R0

UniProt ID: C7LMU5

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
  • EcoCyc, EcoCyc
  • Retrieved from "http://e80boot.org/index.php?title=EG13275_EPinilla&oldid=15660"