MMSYN1 0109

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Author Information

Kyu seo Ahn

Basic Information

  • ID: MMSYN1_0109
  • Name: apn1
  • Organism: JCVI-Syn3.0
  • Description: Could not find this entry in uniprot. Very little is actually known about the functionality about this gene. What we do know is that Endonuclease IV plays a role in DNA repair. 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.
  • DNA Length: 867 base pairs.
  • DNA sequence:

atgaacaaagtgctgctgggctgccatgtgagcatgaacaaacagaacaactatctggtg ggcagcgtgaacgaagcgattagctataaagcgaacacctttatgatttttaccggcccg ccgcagagcaccctgcgcaccaacaccaaccatctgtatattaaccagatgcatgaactg atgaacagctataaaattgatgcgaaagatctggtggtgcatgcgccgtatattattaac attgcgaacagcgtggatcagaacaaatggaaatttgcggtggattttctgattcaggaa attaaacgctgcgaagaaattaaaattccgaccctggtgctgcatccgggcagccatacc accggcaactataaagatagcctgaaccagattattaaagcgctggatattgtgagcaac tatcaggtgaacgtgaaaattgcgctggaaaccatgagcggcaaaggcaccgaagtgtgc agcaaactggaagattttaaatatattctggataacgtgaaaaacaaagataaagtgggc gtgtgcctggatacctgccatctgcatgatgcgggctatgatctgagcaaatgggatgaa tttaaagaacagatgaaacagaactttgatctgaacaaagtgctgtgcattcatctgaac gatagcaaaaacatgattagcagccataaagatcgccatgcgaacattggctatggctat gtgggctttgataccctggtgaacgtggtgtttgataaagattttagcaacattagcaaa attctggaaaccccgtatattgataaaaaaccgccgtataaaattgaaattgaagatctg ctgaacaaaacctttaccaaccgcctgtaa

  • Amino Acid length: 289 amino acids.
  • Amino Acid sequence:

MNKVLLGCHVSMNKQNNYLVGSVNEAISYKANTFMIFTGPPQSTLRTNTNHLYINQMHELMNSYKIDAKDLVVHAPYIINIANSVDQNKWKFAVDFLIQEIKRCEEIKIPTLVLHPGSHTTGNYKDSLNQIIKALDIVSNYQVNVKIALETMSGKGTEVCSKLEDFKYILDNVKNKDKVGVCLDTCHLHDAGYDLSKWDEFKEQMKQNFDLNKVLCIHLNDSKNMISSHKDRHANIGYGYVGFDTLVNVVFDKDFSNISKILETPYIDKKPPYKIEIEDLLNKTFTNRL

Function and Homologs

  • Product: apurinic endonuclease
  • Module: apurinic endonuclease
  • 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: 1665/Ident.: 100.0%/Positives : 100.0%/Query Length: 312/Match Length: 312, http://www.uniprot.org/uniprot/F0V2J1

    • Probable endonuclease 4

E-value: 0.0/Score: 1628/Ident.: 97.7%/Positives : 99.4%/Query Length: 312/Match Length: 317, http://www.uniprot.org/uniprot/F0QS93

    • Probable endonuclease 4

E-value: 6.4e-131/Score: 996/Ident.: 61.6%/Positives : 75.9%/Query Length: 312/Match Length: 322, http://www.uniprot.org/uniprot/I6YM89

Expression

  • Expression Level: High
  • 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 high expression of the gene.
  • Expression Level References and Description: I found the gene's expression level in Mycoplasma genitalium simulation results (http://e80boot.org/index.php?title=File:MgenitaliumSimProteinCounts.xlsx) using its synonym, nfo. In order to form my hypothesis, I examined the function of this gene's module.
  • 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.
  • Dependencies: In order for the functional module to repair DNA, removal of the damaged base by a cleavage of the glycosidic bond by a glycosylase enzyme generating an apyyrimidinic must first occur (https://biocyc.org/gene?orgid=ECOLI&id=EG10651). Thus, a dependent gene, one gene that participates in the creation of such a cleaver, is AlkA (https://en.wikipedia.org/wiki/DNA_glycosylase).
  • 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