MMSYN1 0097

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Author Information

Ashley Westerfield

Basic Information

  • ID: MMSYN1_0097
  • Name: 5'-3' exonuclease, N-terminal resolvase-like domain protein
  • Organism: JCVI-Syn3.0
  • Description: DNA Polymerase I (Pol I) is a multifunctional enzyme that combines a DNA polymerase activity, a 5' to 3' exonuclease activity and a 3' to 5' proofreading exonuclease activity. It is required for several types of DNA repair and appears to be the primary enzyme responsible for stripping RNA primers from newly-synthesized DNA and replacing them with DNA [1]. Interestingly, DNA polymerase I is responsible for both a 5’ to 3’ exonuclease activity and a 3’ to 5’ proofreading exonuclease activity. This gene probably encodes for the 5' to 3' exonuclease capability [2].
  • DNA Length: 912 base pairs.
  • DNA sequence:

ATG ATC ACT AAC GAG ACT AAA CCT ATT TTA CTT ATC GAT GGG TAC CAT TTA TTA CAC AAG GGA TAT TAC GGC ACA CTG AAG CGT ACC ATC GTC TCC AAA AAT AAA GAC GGT ATT GTG ATT AAC GCA ATT TAC AGT TTT GTA GCA AAC ATC TTA AAA TTT GTG CAG TCA GAT CGT TAT CAC TCC GTT ATT GTG GCT TTT GAC TTT GAC GAG AAT TGC TGG CGT AAA GAA CTG TAC TCA GAG TAT AAA GCC AAA CGT AAA CCA ACC CCA ATC GAC TTG GTG CCA CAG CTT CAG ATT GCG CGT GAT TTT CTT ACT TCT GCG AAC ATC TCT TGG TAT GAA AAA TAC AAC TAC GAG GGG GAT GAC GTT ATC GGG TCC ATC TGC CGC ATC GCC AAC AAG CTT GGG TAC GAT GTA TGC ATC CTT ACT AAT GAC AAA GAC ATT TAC CAG TTA GTG AAC AAT AAA ACA TCA ATT ATC ACG AAT ATC TCA AAA AAG GAA AAA ACC AAG ATT ATC AAA CCT CAA CAG GTG TAC GAG CAT TTT TTA TGC CAG CCC AAT CAG GTA GCA GAC ATC AAA GCA ATC TTA GGC GAT CAG TCA GAT AAT ATC AAG GGG GTG AAG TAC ATC AAG CGT AAA CAA GCT GAG AAC CTG ATC AAC AAG TAC GAA AAT GTA GAA AAT ATT CTT GCT CAC ATC AAT GAG TTG AAC GAG CCT CTT AAG ACG ATT ATC AGT GAA AAT AAA CAG TTG ATC ATC GAT AAT AAA AAG ATC ACC AAA ATT CTG ACC AAT GTA AAA CTT GGC CGT ATC AAC TTC AAG CCA ACG AAG ATC ACT TAC TAC GGT CTT ATT CGC TTC CTG AAA GAG CAA GAG ATG TAC GCT TTC ATT AAG CCT ATT CGC CGC TAC CTG GAC CGC ACA AAC AAA AAT CTG AAG AAA TAA

  • Amino Acid length: 303 amino acids.
  • Amino Acid sequence:

MITNETKPILLIDGYHLLHKGYYGTLKRTIVSKNKDGIVINAIYSFVANILKFVQSDRYHSVIVAFDFDENCWRKELYSEYKAKRKPTPIDLVPQLQIARDFLTSANISWYEKYNYEGDDVIGSICRIANKLGYDVCILTNDKDIYQLVNNKTSIITNISKKEKTKIIKPQQVYEHFLCQPNQVADIKAILGDQSDNIKGVKYIKRKQAENLINKYENVENILAHINELNEPLKTIISENKQLIIDNKKITKILTNVKLGRINFKPTKITYYGLIRFLKEQEMYAFIKPIRRYLDRTNKNLKK

Function and Homologs

  • Product: DNA polymerase I, 5'-3' exonuclease
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches. (based on UniProt BLAST)
    • DNA polymerase I, 5'-3' exonuclease (Mycoplasma capricolum subsp...), 1381/100%/0.0/86.6%, A0A084EQK5
    • 5'-3' exonuclease, SAM domain protein (Mycoplasma leachii (strain D..), 1361/100%/0.0/85.6%, E4PT59
    • DNA polymerase I, 5' 3' exonuclease (Mycoplasma feriruminatoris), 1350/100%/0.0/84.2%, L5L9G6
  • Equivalent E. coli / JCVI functional protein: EG10746

This EcoCyc code is for DNA polymerase I (or polA). However, all BLAST searches indicate that this homolog only has ~30% alignment with this JCVI gene, which explains why the page for EG10746 does not link back to this JCVI gene page. This may mean that my gene is a partial component of DNA polymerase I.

Expression

  • Expression Level: Medium
  • Expression Level Hypothesis: DNA polymerase is essential for maintenance of the DNA, especially during replication.
  • Expression Level References and Description: During my BLAST alignment for this gene sequence, the closest gene to align with this sequence was polA, which encodes DNA polymerase I. As a result, I used the results for polA in the M. genitalium database, even though this gene is probably not polA (it could be an ancillary gene or protein that is associated with polA).
  • Expression Time: Late
  • Expression Time Hypothesis: DNA polymerase is important during replication, which is a process that occurs late in the the lifespan of a cell.
  • Expression Time References and Description: Gene description (assuming that it is, or is related to polA); however, I am not sure of the exact identity of this gene.

Gene Context

  • Possible Dependencies: DNA metabolism; if DNA is not synthesized in the cell, then DNA polymerase cannot edit/repair any DNA. Given that this gene is specifically an exonuclease, it requires nucleotides in order to function. More DNA that is present in the cell means more DNA polymerase I activity.
  • Process: 5'-3' exonuclease activity
    • Inputs: Deoxynucleoside triphosphate + DNA(n)
    • Outputs: diphosphate + DNA(n+1)

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
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10746-MONOMER
  • [3]
  • Retrieved from "http://e80boot.org/index.php?title=MMSYN1_0097&oldid=14659"