MMSYN1 0006

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Author Information

Julia Schaepe

Basic Information

  • ID: MMSYN1_0006
  • Name: gyrB
  • Organism: JCVI-Syn3.0
  • UniProt ID: [1]
  • Description: GyrB produces an enzyme called DNA gyrase subunit B, which is necessary subunit of DNA gyrase. On a larger scale view, DNA gyrase is a DNA topoisomerase which classifies all enzymes that catalyze the winding and unwinding of DNA strands, functions important and necessary for protein synthesis (https://www.ebi.ac.uk/interpro/potm/2006_1/Page1.htm). DNA gyrase negatively supercoils circular double-stranded DNA using ATP to maintain chromosomes in an underwound state (http://www.uniprot.org/uniprot/P0AES6). Maintaining the underwound state, which means that there are fewer helical turns in the DNA than would be expected in the B-form structure, is necessary to create the strain responsible for supercoiling (http://www.bioinfo.org.cn/book/biochemistry/chapt23/bio2.htm). Supercoiling is the coiling of an already coiled DNA structure, which affects the overall function of DNA by altering the epigenetics of DNA. 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). Underwinding of DNA makes it easier to separate DNA strands and perform replication and transcription. It is also possibly involved in decatenation of newly synthesized chromosomal and plasmid DNA. Decatenation is the process of separating the physical linkage between the two topologically linked-daughter chromosomes that are created in replication. Its primary partner in the cell is DNA gyrase subunit A. The A and B subunits both bind to DNA, hydrolize ATP, and create the negative supercoils. B specifically, though, is responsible for the negative supercoils. GyrB contains the gyrase ATPase activity and is the binding site for antibiotics that inhibit gyrase function (https://ecocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CPLX0-2425). The ATPase active site is also only located on the GryB subunit, meaning that substrates, primarily aminocoumarins, binding to DNA gyrase subunit B inhibits all the functions of gyrase (https://en.wikipedia.org/wiki/DNA_gyrase).
  • DNA Length: 1902
  • DNA sequence (codon optimized) :

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

  • Amino Acid length: 634
  • Amino Acid sequence:

MSQEYSAESIKVLKGLEAVRTRPGMYIGSTSKTGLHHLVWEILDNSIDEAMAGYADLINVTITKENEVIVQDNGRGIPVGINSDTKKSALSLVFTQLHAGGKFDSETYKISGGLHGVGASVVNALSLYVEVEVYRNNIHYHQLFSEGGTKESELQQLGHTDLRGTKVKFKPDPEIFKETVVFDYEIIKNKVKQLAFLNKGLKITLTDERIEKTVEYLFLNGILDYIKEKNETKNKINPNIFYVDSKYEDIEVEMALQYNSDYQENIITFVNNINTHEGGTHEDGLKQALIRDINRYADTVIKNNKTPSKFSWDDIKEGMMCILSVRHTDPQYEGQTKTKLSNPDAKEAVNIIIGNAFEEFLLKSPEDAKAILDKNVNAQKARIAAQKAREETRRKSALDSFSLPGKLADCETKDSSIAELYLVEGDSAGGSAKTGRNRKFQAILPLRGKVLNVERVTEARAFSNNEIKSIITAVGTGIKEELDLSKLRYKKIVIMTDADVDGAHIRTLLLTFFYRYMKPLVANGHIYIAQPPLYKIEAGKKIAYAYTDSQLDELKNNEFNNLKYTIQRYKGLGEMDPLQLWETTMDPQQRTMLQISLEDATLANEVFSDLMGEDPELRKIYIQDNAKFVENIDF

Function and Homologs

  • Functional Category: DNA topology
  • Product: DNA gyrase subunit B
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA gyrase subunit B [Mycoplasma mycoides] / 1285 / 99% / 0.0 / 99% / WP_020862421.1
    • DNA gyrase subunit B [Mycoplasma mycoides] / 1281 / 99% / 0.0 / 99% / WP_013729164.1
    • DNA gyrase subunit B [Mycoplasma mycoides] / 1281 / 99% / 0.0 / 99% / WP_015545273.1
  • Equivalent E. coli / JCVI functional protein: EG10424

Expression

  • Expression Level: medium
  • Expression Level Hypothesis: Since DNA gyrase is important in DNA replication and transcription, but is not one of the most essential aspects, it is relatively important within the cell and should be expressed at a medium level.
    • Expression Level References and Description: This data was gathered from the Mycoplasma genitalium simulation protein counts [2].
  • Expression Time: late
  • Expression Time Hypothesis: This should be expressed late in cell life since gyrB is predominantly involved in cell replication, which is important only late in the life of a cell.
    • Expression Time References and Description: This data was gathered from the Mycoplasma genitalium simulation protein counts [3].

Other Components

Required component: gyrA, DNA gyrase subunit A MMSYN1_0007.

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

Dependencies

Dependency: Oxidative phosphorylation.

Gyrase subunit B is dependent on the existance of ATP in order to perform its manipulation of DNA, and therefore oxidative phosphorylation, which synthesizes ATP is necessary [5].

Process

Process: a double stranded DNA + ATP ⇄ a negatively supercoiled DNA + ADP + phosphate

Input: a double stranded DNA, ATP

Output: a negatively supercoiled DNA, ADP, phosphate

The left side of the reaction indicates the input, and the right side indicates the output after gyrB 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