MMSYN1 0452

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Author Information

Julia Schaepe

Basic Information

  • ID: MMSYN1_0452
  • Name: parE
  • Organism: JCVI-Syn3.0
  • UniProt ID: [1]
  • Description: Topoisomerase IV subunit B is a subunit of the enzyme Topoisomerase IV. This enzyme is necessary for DNA replication to be enacted. This enzyme is essential for chromosome segregation because its main function is decatenating newly replicated chromosomes. Decatenation is the process of separating the physical linkage between the two topologically linked-daughter chromosomes that are created in replication. The enzyme accomplishes this by relaxing supercoiled DNA (http://www.uniprot.org/uniprot/P20083). Supercoiling is the coiling of an already coiled DNA structure. Supercoiling also allows DNA to form a more compact and stable structure (useful to stabilize during replication and transcription) (http://highered.mheducation.com/sites/0072995246/student_view0/chapter20/action_of_dna_gyrase.html). DNA is in a relaxed state if the helix has a normal number of base pairs per helical turn. DNA can become over or under twisted (also known as over or under wound) (https://tandem.bu.edu/knex/supercoil.knex.html). If the DNA forms a circular molecule or a loop, this causes supercoiling. Essentially, when Topoisomerase IV is decatenating the newly replicated chromosomes, it is undoing the supercoiling and reverting the DNA to its relaxed state. A protein called MukB stimulates the relaxation activity of topoisomerase IV. Topiosomerase IV performs a similar function to DNA gyrase in that they both relax positive supercoils (overwound DNA) (https://en.wikipedia.org/wiki/Topoisomerase_IV).
  • DNA Length: 1392 base pairs
  • DNA sequence:

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

  • Amino Acid length: 643 amino acids
  • Amino Acid sequence:

MAENKKYDESAIQVLEGLDAVRKRPGMYIGSTDNRGLHHLVWEIVDNAIDEALAGYCTQIDVILEKDNSITVIDNGRGIPTGMHKTGKSTPEVIFSVLHAGGKFDSTAYKSSGGLHGVGSSVTNALSKRFKATIYRDKKIHEIEFKNGGKLEKPLTFIANTYKTGTTINFLPDDSIFSNTKFNFSLISERLKESALLNSGLKITLSDLISNRYVEYQFQDGLVEFIKELVDDKTPVTDIITINNESKNIIAEIALQYTEDDNEIILGFANNVKTSDGGTHLVGFKSGLIRAINDYAKDQKILKDKTKLDSNDLREGLVAIVTVKIPENLIEYEGQTKSKLGTSDAKTVVEQIVYEFMSYWLIENKVLANKVIENALNAQKARIAAKQARQAIKSVKGKKNVNKLMLGKLTPAQGKKRELNELYLVEGDSAGGSAKSGRDRNFQAILPLRGKVINSEKAKLVDLLKNEEIQSIINAIGAGVGKDFDISDINYGKIIIMTDADTDGAHIQTLLLTFFYRHMKDLITHKKVYIALPPLYKITFNDKSFIYLWDEEELNEFNKTNTKKYEIQRYKGLGEMNADQLWQTTMDPKNRKIIQVSISDGLLAERMFKTLMGDDVEKRKLWIQENVKFTLEDDQIQIIEMEK

Function and Homologs

  • Product: DNA topoisomerase IV subunit B [Mycoplasma mycoides]
  • Module: [Topoisomerase]
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA topoisomerase IV subunit B [Mycoplasma mycoides], 1278/99%/0.0/99%, [WP_013729613.1]
    • DNA topoisomerase IV subunit B [Mycoplasma mycoides], 1277/99%/0.0/99%, [WP_017697794.1]
    • DNA topoisomerase IV subunit B [Mycoplasma capricolum], 1259/99%/0.0/97%, [WP_046784060.1]

Expression

  • Expression Level: medium
  • Expression Level Hypothesis: DNA Topoisomerase is essential for DNA replication, and therefore should be relatively prevalent within the cell.
    • Expression Level References and Description: This data was gathered from the Mycoplasma genitalium simulation protein counts [2].
  • Expression Time: late
  • Expression Time Hypothesis: DNA Topoisomerase is essential for DNA replication and can remove double-stranded DNA crossings, decatenating the DNA daughter molecules. This process begins to occur late in the cell's life cycle. ** Expression Time References and Description: This data was gathered from the Mycoplasma genitalium simulation protein counts [3].

Other Components

Required component: parC, DNA topoisomerase IV subunit A MMSYN1_0453

DNA topoisomerase IV subunit A is the only other component that combines with subunit B to form DNA topoisomerase IV, the necessary enzyme [4].

Dependencies

Dependency: DNA replication

DNA topoisomerase IV subunit A is a subunit of DNA topoisomerase, of which one of the main functions is decatenating topologically linked daughter DNA molecules that are the product of DNA replication [5].

Process

Process: topologically daughter DNA molecules + ATP ⇄ 2 daughter DNA molecules + ADP + phosphate

Input: topologically daughter DNA molecules, ATP

Output: 2 daughter DNA molecules, ADP, phosphate

The left side of the reaction indicates the input, and the right side indicates the output after parE performs its main function [6].

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