EG10651

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Author Information

Kyu seo Ahn

Basic Information

  • ID: EG10651
  • Name: nfo
  • Organism: E. coli
  • Description: Endonuclease IV, the functional unit for the gene, plays a role in DNA repair. It focuses on damaged bases in DNA that have occured due to alkylating agents, ionizing radiation or oxidants such as superoxide radicals, hydrogen peroxide and hydroxyl radicals. Base excision repair (BER) works to repair damaged DNA by multiple steps: removal of the damaged base by a cleavage of the glycosidic bond by a glycosylase enzyme generating an apyyrimidinic or apurinic (AP) site; removal of the AP site by an AP endonuclease; resynthesis of the excised strand by DNA polymerase using the intact strand as template and ligation by DNA ligase. Nfo is one of two (the other being XthA) 5' AP endonucleases in Escherichia coli . It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin (https://biocyc.org/gene?orgid=ECOLI&id=EG10651).
  • DNA Length: 855 base pairs.
  • DNA sequence:

atgaaatatattggcgcgcatgtgagcgcggcgggcggcctggcgaacgcggcgattcgc gcggcggaaattgatgcgaccgcgtttgcgctgtttaccaaaaaccagcgccagtggcgc gcggcgccgctgaccacccagaccattgatgaatttaaagcggcgtgcgaaaaatatcat tataccagcgcgcagattctgccgcatgatagctatctgattaacctgggccatccggtg accgaagcgctggaaaaaagccgcgatgcgtttattgatgaaatgcagcgctgcgaacag ctgggcctgagcctgctgaactttcatccgggcagccatctgatgcagattagcgaagaa gattgcctggcgcgcattgcggaaagcattaacattgcgctggataaaacccagggcgtg accgcggtgattgaaaacaccgcgggccagggcagcaacctgggctttaaatttgaacat ctggcggcgattattgatggcgtggaagataaaagccgcgtgggcgtgtgcattgatacc tgccatgcgtttgcggcgggctatgatctgcgcaccccggcggaatgcgaaaaaaccttt gcggattttgcgcgcaccgtgggctttaaatatctgcgcggcatgcatctgaacgatgcg aaaagcacctttggcagccgcgtggatcgccatcatagcctgggcgaaggcaacattggc catgatgcgtttcgctggattatgcaggatgatcgctttgatggcattccgctgattctg gaaaccattaacccggatatttgggcggaagaaattgcgtggctgaaagcgcagcagacc gaaaaagcggtggcgtaa

  • Amino Acid length: 285 amino acids.
  • Amino Acid sequence:

MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYH YTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEE DCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDT CHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIG HDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQTEKAVA

Function and Homologs

  • Product: Endonuclease 4
  • Module: Endonuclease 4
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Probable endonuclease 4

E-value: 0.0, Score: 1492, Ident.: 100.0%, Positives : 100.0%, Query Length: 285, Match Length: 285, http://www.uniprot.org/uniprot/A0A0M7N8S9

    • Probable endonuclease 4

E-value: 0.0, Score: 1492, Ident.: 100.0%, Positives : 100.0%, Query Length: 285, Match Length: 285, http://www.uniprot.org/uniprot/S1HGJ6

    • Probable endonuclease 4

E-value: 0.0, Score: 1492, Ident.: 100.0%, Positives : 100.0%, Query Length: 285, Match Length: 285, http://www.uniprot.org/uniprot/D8BXF8

Expression

  • Expression Level: Medium
  • Expression Level Hypothesis: The functional module this gene is part of is involved in DNA repair. DNA maintenance is incredibly important for the survival of an organism and thus we require a moderate expression of the gene.
  • Expression Level References and Description: I found the gene's expression level in Escherichia coli proteome dataset (http://e80boot.org/index.php?title=File:EcoliProteomicExpressionData.xlsx). In order to form my hypothesis, I examined the function of this gene's module. I also checked against other genes in this functional category and it seemed like most DNA repair genes had a medium expression level.
  • Expression Time: Late
  • Expression Level Hypothesis: The cell does not need to immediately correct for small errors in the DNA.Small scale DNA degradation is often the result of time and decay, so it follows that this protein should be expressed later on the the cell lifecycle.
  • Expression Time References and Description: In order to form my hypothesis, I examined the function of this gene's module (described in part I).

Gene Context

  • Other components: This gene codes for the functional module by itself. It requires no other components to function.
  • Process: cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues.

Inputs: a single stranded DNA + n H2O Outputs: n a 5'-phosphooligonucleotide Reference: Function section of http://www.uniprot.org/uniprot/P0AC28. Reaction section of https://biocyc.org/gene?orgid=ECOLI&id=EG10651#tab=RXNS

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