MMSYN1 0859

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Author Information

Sruthi Raguveer

Basic Information

  • ID: MMSYN1_0859
  • Name: topA
  • Organism: JCVI-Syn3.0
  • Description: This gene codes for DNA topoisomerase I. Topoisomerases are an essential group of proteins that deal with DNA topology. DNA topoisomerase I relaxes supercoiled DNA and hence relieves torsional tension that is created during replication and translation UniProt. The topoisomerase achieves this through creating a single strand break in the duplex DNA through transesterification that allows one strand to remove its supercoils. The DNA is then religated and the phosphodiester backbone is restored.
  • DNA Length: 1962 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 653 amino acids.
  • Amino Acid sequence:

MKVLVLLESPSKIEKIKHYLEESFPENQFVVLASGGHINSIADKGAWGLGIDLETMQPDFVIDSSRKKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLKDIDMNLVNAQISRQILDKIIGYLVSKSLQKSTGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKRAINLSLVKDKNNVLVNTEKTYYIDEKQAKAIVDELGEVYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFISEVKDYISKNYSSDLFKAPVVGKKDQNSQEAHESIRPTNIWLTPEKASLEIEDNLLKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAIKHSSSDENIELTDDGEEVVKTKDPKPEYQFNDDFEINISKKYIKIEDAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEFPKSKPIVVTNKGYSANQYLYDHYLDFFNLNYTAEMEEKLDEITKGSFDYVNWLKEIYNALNIKVKKEIGEAKTEAICPRCGANLVYIKSRFNRGRGCSNFTKTKCGYREYEQPDGTWKEYVKEEKPQEESSTETKSTKKSKTKKDNK

Function and Homologs

  • Product: DNA Topoisomerase 1
  • Closest homologous proteins:
    • DNA topoisomerase I (Mycoplasma capricolum), 1231/96%/0/96%, WP_046784256.1
    • DNA topoisomerase I (Mycoplasma leachii), 1225/96%/0/95%, WP_014584532.1
    • DNA topoisomerase I (Mycoplasma feriruminatoris), 1201/97%/0/93%, WP_008363616.1
  • Equivalent E. coli / JCVI functional protein: EG11013

Expression

  • Expression Level: high
  • Expression Level Hypothesis: The gene expression for topA is likely high because it removes supercoiling due to replication and translation which is necessary to maintain DNA integrity. Translation is constantly occurring within a cell.
  • Expression Level References and Description: M. genitalium model data
  • Expression Time: early
  • Expression Time Hypothesis: This gene should be expressed early because translation will occur at the beginning stages of the organism's life in order to produce integral proteins and this protein must exist for the DNA post-translation to have the proper topology.
  • Expression Time References and Description: UniProt Elsevier

Gene Context

  • Other Components: There is only one protein in this functional module. No other components are necessary.
  • Possible Dependencies: RNA Polymerase DNA Topoisomerase 1 is mainly functional after translation and replication and so is likely dependent on polymerases.
  • Process: The main process is the relaxation of supercoiled DNA
    • Inputs: Supercoiled DNA, Mg2+
    • Outputs: Normal DNA
    • References: UniProt

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file