MMSYN1 0824 rperez4

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Author Information

Reinaldo Perez

Basic Information

  • ID: MMSYN1_0824.
  • Name: uvrA: excinuclease ABC subunit A.
  • Organism: JCVI-Syn3.0.
  • Description: The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate (Source).
  • DNA Length: 2841 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 946 amino acids.
  • Amino Acid sequence:

MSTDKIIIKGAREHNLKNIDLELPKNKLIVFTGLSGSGKSSLAFSTIYQEGRRRYIESLSAYARQFLGGNEKPDVDSIEGLSPAISIDQKTTSHNPRSTVGTVTEIYDYLRLLYARIGQPYCINNHGQIKAVSIKEIVENIKQSTSDGEQIHILSPVIRDKKGTHIDILEKLRNDGFIRVIVDDQLRMLDDQINLEKNQRHNIDIVVDRIIYHNNDEINSRIFTAVEMGLKYSNNLIKIAFPNSNKQEKLFSTSFSCKVCDFVVPELEPRLFSFNAPLGACELCNGLGVSLEPDINLILPDLKLSINQGGVVYYKNFMHTKNIEWQKFRILCDYYYIDLNTPLKDLTQKQRDIILWGSDREIDIKIVTENNNKYEKYDFIEGNAALIKRRYFESKSEEARKWYSKFMSSKICKQCKGSRLNDIALSVKINEKSIFDYTNMSISEQLDFLLNIDLTPTQATIAKLVLDEIISRTNFLNEVGLGYLNLSRTATTLSGGESQRIRLAKQIGSQLTGILYVLDEPSIGLHQKDNDKLIKTLKHLRDLGNTLIVVEHDEDTMKSSDWIVDIGPRAGEYGGEITFSGTYQDILKSDTITGRYLSRKEGIVVPKTRRGGNGKKIEIIGASENNLKNINVTIPLNKFITITGVSGSGKSTLLEDIVYKGIHNNLSKEYLPIGKVKEIKGIENINKAIYISQEPIGKTPRSNPATYTSVFDDIRDLFTNLPEAKIRGYKKGRFSFNVSGGRCEHCQGDGVITISMQFMPSVEVVCEICEGKRYNDETLTVKYKNKSIADVLNMSVSEAYVFFENIPQIKQKLETILEVGLGYIKLGQNATTLSGGESQRIKLSTYLLKKQTGNTMFLLDEPTTGLHVDDVKRLIGVLNKLVDLGNTVLCIEHNLDFIKVSDHIIDLGPDGGEYGGQVVVTGTPEQIINHPTSYTAKYLKDYIIND

Function and Homologs

  • Product: uvrABC system protein A.
  • Closest homologous proteins:
    • Nexcinuclease ABC subunit A [Mycoplasma capricolum], Max score: 1919/Query Cover: 100%/E-Value: 0.0/Ident: 99%, WP_011387607.1
    • ABC-ATPase UvrA [Mycoplasma capricolum], Max score: 1917/Query Cover: 100%/E-Value: 0.0/Ident: 99%, WP_036432448.1
    • excinuclease ABC subunit A [Entomoplasma melaleucae], Max score: 1481/Query Cover: 99%/E-value: 0.0/Ident: 76% WP_084485280.1
  • Equivalent E. coli functional protein: EG11061.

Expression

  • Expression Level: medium.
  • Expression Level Hypothesis: Since the UvrABC repair system catalyzes and processes DNA lesions, a medium expression level is correlated with relatively medium frequency of DNA lesions. See uvrC protein for similar description of the uvrABC DNA repair system.
  • Expression Level References and Description: This information was gathered from the Mycoplasma genitalium cell model file. I am somewhat uncertain that the expression level will remain so throughout the life cycle of the cell given that a lot more transcription (a possible source of lesions) happens during division which will increase the demand for the repair system.


  • Expression Time: late.
  • Expression Time Hypothesis: The repair mechanism that the UvrABC system performs will not be needed until the cell is already established, the DNA is been regularly transcribed (a possible source for lesions), and there is a higher mutation rate. However, low expression might be useful at an early stage to recognize and repair any fragments that might get damaged at the start of the process.
  • Expression Time References and Description: I decided the expression time to be late because I consider that this gene's function is not necessarily vital at the early stage of the process. I based my judgement on information about DNA repair and additional description of exonuclease activity of the uvrABC system.

Gene Context

  • Other Components: uvrA; uvrC.
  • Possible Dependencies: helicase. The module requires helicase to remove the lesioned DNA once it has been excised.
  • Process: DNA repair of UV damaged light.
    • Inputs: lesioned DNA nucleotides.
    • Outputs: repaired DNA.

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