MMSYN1 0221

From BioE80 Boot
Jump to: navigation, search

Author Information

Anjini Karthik

Basic Information

  • ID: MMSYN1_0221
  • Name: pykF (pyruv_kin or pyruvate kinase)
  • Organism: JCVI-Syn3.0
  • UniProt ID: C7LM85 [1]
  • Description: The gene pykF codes for pyruvate kinase I, an enzyme that is essential for glycolysis, a pathway that generates ATP. The formation of pyruvate and ATP with the help of pyruvate kinase I is the last and crucial step in the pathway and is irreversible under physiological conditions. This gene works with a sister gene, pykA, which codes for pyruvate kinase II; but the two enzymes are not interchangeable, as they are activated by different substrates. Pyruvate kinase I has demonstrated activation by fructose and is often targeted in metabolic engineering due to the key role it plays in controlling metabolic flux in glycolysis [[2]]. Thus, this gene must function for cellular respiration to occur, the main method for a cell to extract and use energy.
  • DNA Length: 1437 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 478 amino acids.
  • Amino Acid sequence:

MTKETLQKRMKRTKVITTIGPSTHSAEAIKELFNNGMTTIRLNFSHGSYEEHGYRIKAAKKISKALNKPISIILDTKGPEIRLGKFKDNKQEVVKGQSITIYTDTYSYLNKECVQGEMTVAYDMSVDLKPGDMILIDDGKLELTVDSVEPQIIKATAFNHHIVKTNKRVNLPGIDFSLPFLSEKDEKDILFGCEQGVDYIAASFVNTAENVRQIKEILNKANANHIQIISKIESQVGLDNIDEIIEESDGIMIARGDLGLEIPYYDVPYWEKIIIRKCREKGKIVIVATQMLETMTENPSPTRAEVTDVYFATELGADATMLSGESAAGDYPFLTVHTMSTINKRAEVEFYNKIYYQVQLDNARNSTSGPRAEIADLLATKTKDGEYKYAIVLSKTGELLKTISKFRPNVTILGVSPDKKLWTSFGVWHSIFMNKVDTLDNLDNNIEKLSEIAKSWGAKLGEKVLVVRSTAIKEIEVI*

Function and Homologs

  • Product: Pyruvate kinase I (also known as pyruvate kinase Type F, type I pyruvate kinase)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Pyruvate kinase (Mycoplasma mycoides), 981/100%/0.0/99%, [3]
    • Pyruvate kinase (Mycoplasma capricolum), 978/100%/0.0/99%, [4]
    • Pyruvate kinase (Mesoplasma florum), 758/99%/0.0/75%, [5]
  • Equivalent E. coli / JCVI functional protein: EG10804.

Expression

  • Expression Level: Low
  • Expression Level Hypothesis: pykF codes for pyruvate kinase I, an enzyme that is activated by fructose and catalyzes glycolysis. However, it may still have a low expression level because a different gene, pykA, codes for pyruvate kinase II, which is activated by glucose; glucose is the preferred fuel of most cells, so pykF is less necessary in comparison.
  • Expression Level References and Description: This information is based on the M. genitalium dataset.
  • Expression Time: Early to middle
  • Expression Level Hypothesis: pykF is not necessary until the organism has already taken in a source of fuel (such as a sugar). Intake must happen first. However, glycolysis is the first step in the photosynthetic pathway, so this gene overall should be expressed in the early to middle stage.
  • Expression Time References and Description: Resources used were the same as those cited in the “Basic Information/Description” section.

Gene Context

  • Other Components: pykA, which codes for pyruvate kinase II, is one other gene needed for the module to work— there was no explicit JCVI pykA gene found, but a close relative is linked here [[6]]
  • Possible Dependencies: hprK: Sugars must be present along with molecules like ADP to enable pyruvate kinase to convert the sugar source into pyruvate and energy in the form of ATP. [[7]]
  • Process: Cellular respiration
    • Inputs: Fructose 1,6-bisphosphate, ADP
    • Outputs: Pyruvate, ATP
    • Resources: Resources used were the same as those cited in the “Basic Information/Description” section.

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