MMSYN1 0515

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Author Information

Addie Petersen

Basic Information

  • ID: MMSYN1_0515
  • Name: dctD
  • Organism: JCVI_Syn3.0
  • Description: This protein encodes an allosteric enzyme that catalyzes the deamination of dCMP to dUMP, which is the nucleotide substrate for thymidylate synthase [1]. By providing the substrate for thymidylate synthase, dCMP deaminase indirectly allows the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP), which preserves the ratios of deoxynucleotides and prevents DNA damage [2]. dCMP deaminase requires a zinc cofactor for binding [3].
  • DNA Length: 480 base pairs.
  • DNA sequence:

ATG TCA AAA CGC CTT GAT TAT CTT AGC TGG CAA CAT TAC TTT ATG CTT ATC GCA AAA GCA TCA GCA ATG CGC TCG AAG GAT CCA AAC ACC CAA GTC GGCGCC ATT GTT GTA AAC GAG TTG CAG CAA ATC GTC GCT ACC GGG TAT AAT GGA TTC CCG CGC GGC GTT TCG GAC GAT GAA TTT CCG TGG TCC AAA AAT AATGAA GAT TGG CTG GAA AAC AAA TAC GCA TAC GTA GCT CAT GCG GAG CTT AAT GCC ATT GTC AGT TCC CGC TCC GAC TTA TCG AAC TGT GAC CTT TAC GTAACC CTG TTC CCC TGT AAT GAA TGC GCC AAG ATC ATT ATC CAG GCG GGA ATT AAG CGC ATC TAT TAT GCG AAC GAT CCA TAC CAT GAC AAA AAG GAG TTTATT GCT TCC AAG AAA ATG CTT GAT GCA GTT AAC ATC AAG TAC ATT AAA CTT CCT GAC ATT GAA ATC TCC CTG AAG GTC AAA GAT TAG

  • Amino Acid length: 160 amino acids.
  • Amino Acid sequence:

MSKRLDYLSWQHYFMLIAKASAMRSKDPNTQVGAIVVNELQQIVATGYNGFPRGVSDDEFPWSKNNEDWLENKYAYVAHAELNAIVSSRSDLSNCDLYVTLFPCNECAKIIIQAGIKRIYYANDPYHDKKEFIASKKMLDAVNIKYIKLPDIEISLKVKD

Expression

  • Expression Level: [low]
  • Expression Level Hypothesis: I would hypothesize that dCMP deaminase is lowly expressed because it catalyzes the reaction necessary salvage deoxynucleotides. Although this is an important cellular process, only a few of these enzymes may be necessary to salvage a sufficient number of pyrimidines.
  • Expression Level References and Description: I gathered the information that dCMP deaminase catalyzes the reaction preserve deoxynucleotides, [4] and also found that there is a low number of dCMP deaminases in the M. genitalium whole cell model [5]
  • Expression Time: [early]
  • Expression Level Hypothesis: I would hypothesize that dCMP deaminase needs to be expressed early in the cell cycle because it helps maintain the deoxynucleotide supply. As a steady deoxynucleotide supply is necessary for proper DNA repair and replication, dCMP deaminase needs to be expressed early to provide substrates necessary for processes that occur late in the cell cycle, such as DNA replication and repair.
  • Expression Time References and Description: I gathered the information that dCMP deaminase catalyzes the reaction to maintain a deoxynucleotide supply, [6], and knew that a deoxynucleotide supply was necessary for processes like DNA replication and repair later in the cell cycle, necessitating early expression.

Gene Context

  • Other Components: Module only has 1 component.
  • Possible Dependencies: deoxynucleotides [7]
  • Process: Deamination of dCMP to dUMP
    • Inputs: dCMP
    • Outputs: dUMP, NH2

Function and Homologs

  • Product: dCMP deaminase [8]
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Cytidine deaminase [Escherichia coli], 61.6/77%/5e-10/28%, [WP_044686932.1]
    • Deoxycytidylate deaminase[Escherichia coli], 60.5/77%/1e-09/28%, [ACG59599.1]
    • Cell division protein DedD[Escherichia coli], 52.0/34%/3e-07/45%, [OMI56163.1]
  • Equivalent E. coli / JCVI functional protein: EG10137
  • https://www.ncbi.nlm.nih.gov/gene/1635
  • https://en.wikipedia.org/wiki/Thymidylate_synthase
  • http://www.uniprot.org/uniprot/Q6MT32
  • https://www.ncbi.nlm.nih.gov/gene/1635
  • http://e80boot.org/index.php?title=File:MgenitaliumSimProteinCounts.xlsx
  • https://www.ncbi.nlm.nih.gov/gene/1635
  • http://www.uniprot.org/uniprot/Q6MT32
  • http://www.uniprot.org/uniprot/Q6MT32
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