MMSYN1 0254 rperez4

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Author Information

Reinaldo Perez

Basic Information

  • ID: 0254
  • Name: uvrC
  • Organism: JCVI-Syn3.0
  • Description: The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision (Source).
  • DNA Length: 1755 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 584 amino acids.
  • Amino Acid sequence:

MSLKQQVDLLPNKPGCYLFFNKDNDVIYVGKAKNLKKRVSTYFNKAYNIKTTRLVREITDLKYFIVDNEKESLLLEKNLIKKYHPKYNVLLNDDKTYPYIIITNQKDPMYKYVRKYDKKALKNYGPLPIGSNARSILLTLQRLFPLRMCQGNLNKPCLYYHLNQCSGACFKQVDLSYYEYQIKQVDKFFKGEINQVKQTLIKQMQKASDNLQFEQAQRIKDQITSLDFITAKQNVDIVTNKNIDVINYEINQDKICFVMLFYRLGQLTYKDEYIQNYEGQNLSELFNSYLQQIYQKNIYPDVLLIPNEIELLDLDQNLLEFSSYSLNKQDDVFIKLAKQNAIDSLNKSVISHNVNSGDEIEILEQLKQISNASKYLKRIEIFDISNIYNQFITGACIVYINAKPIRNEFRKYNIDSSYTSDYARMKFMLEKRFLKRIKEKEQLPDLIIVDGGIIQIHAAKEVLNKLNLKIDVIGLSKDDHHKTRYLIDIFEQTIDIKNFKKLYNFLTSLQIRVDEYAKSGFRKKYHNQLNDQILLIKGVGKKTNLKLYKHFKTIDNIKNASFDELNKVINNKKITNLIISNLNK

Function and Homologs

  • Product: UvrABC system protein C.
  • Closest homologous proteins:
    • excinuclease ABC subunit C [Mycoplasma feriruminatoris], Max score: 1066/Query Cover: 100%/E-Value: 0.0/Ident: 93%, Accession
    • excinuclease ABC subunit C [Mycoplasma capricolum], Max score: 1065/Query Cover: 100%/E-Value: 0.0/Ident: 92%, Accession
    • excinuclease ABC subunit C [Mycoplasma leachii], Max score: 1048/Query Cover: 100%/E-value: 0.0/Ident: 91% [WP_013447612.1].
  • Equivalent E. coli functional protein: EG11063.

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. These lesions dont happen too often so there is no need to have a high expression level, but they happen often enough that a low expression level would not be able to keep up.
  • 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 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 the exonuclease activity of the uvrABC system.

Gene Context

  • Other Components: uvrA; uvrB.
  • 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; ATP.
    • Outputs: fixed 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