MMSYN1 0288

From BioE80 Boot
Jump to: navigation, search

Author Information

Luis Fernando Varela

Basic Information

  • ID: MMSYN1_0288
  • Name: hisS
  • Organism: JCVI-Syn3.0
  • Description:

Histidine-tRNA ligase (hisS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. HisRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90, Cusack91].

HisRS is a dimer in solution [Kalousek74]. The C-terminal domain of the protein is required for dimerization, while the N-terminal domain contains most of the catalytic activity. The two domains do not complement each other in trans [Augustine97]. Minimal active site fragments likely representing the ancestral "urzyme" have been studied [Li11h].

Specificity determinants within tRNAHis that are important for recognition by HisRS have been identified; the unique G-1:C73 base pair was found to play a crucial role [Himeno89, Yan94, Fromant00, Rosen04a, Guth07]. Specificity determinants and residues within HisRS that are important for catalytic activity have been investigated [Yan95, Ruhlmann97, Bovee99, Hawko01, Connolly04, Guth07], and a model for the catalytic cycle was proposed [Guth07]. The C-terminal domain of HisRS was found to be largely responsible for recognition of the tRNAHis anticodon [Yan96].

Crystal structures of HisRS have been determined, and a reaction mechanism was proposed [Arnez95, Arnez97]. Various types of experiments support a substrate-assisted concerted reaction mechanism [Guth05]. Catalysis may occur at sites alternating between the two monomers; conformational changes may be rate-limiting for product formation [Guth07, Guth09]. The mechanisms of substrate discrimination [Banik09, Banik10] and the aminoacylation reaction [Banik11] have been modeled.

  • DNA Length: 1242 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 414 amino acids.
  • Amino Acid sequence:

MLQKPRGTQDFFLDEAKLWNKVETKLKEILDQFNYSEIRTPMFESKELFIRSIGSTTDIVSKEMYEFVDKKNRSLVLKPEGTASVVRAVIENKLYKEENLPLKVYYISPMFRYERPQNGRYRQFHQLGIEVFGSDSIQQDYEVLNIATKIINQFKLNENIKIYTNFLITGKNREDYILELKKYLSDFKLCNDCNTRLEKNPLRVLDCKIDDKQFKNVPSMQDFLTKEQKTRYDQTLELFKKTNISVIHDDKLVRGLDYYTGFIFEIKYLNNNNEQTIIAGGRYNNLVNEIGNINLAACGFGMGLERFINIIKEQNSSLVNQKTNIDLYTICIDDLAIELNQQILDLTRSIGLKADSNYYHLSLKSALKKADKLNPKYVIILGSNEAKTNEFIIKDQINKTQIKTTLTKFIKYLK

Function and Homologs

  • Product: Histidine--tRNA ligase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • histidine--tRNA ligase [Mycoplasma feriruminatoris], Max score: 755/ Query Cover: 100%/ E-Value: 0.0/ Ident: 88%, WP_008364475.1
    • histidine--tRNA ligase [Mycoplasma putrefaciens], Max score: 524 /Query Cover: 98% / E-Value: 0.0 /Ident: 98%, WP_015587323.1
    • histidine--tRNA ligase [Entomoplasma somnilux], Max score: 422 / Query Cover: 97% / E-Value: 9e-143 / Ident: 53%, WP_024863302.1
  • Equivalent E. coli functional protein: EG10453

Expression

  • Expression Level: low
  • Expression Level Hypothesis: This interprets the genetic code by covalently linking amino acids to their specific tRNA molecules, which seems to be something that we don't need too frequently.
  • Expression Level References and Description: M. genitalium model data
  • Expression Time: Right at the beginning
  • Expression Level Hypothesis: Since this is a member of the family of aminoacyl-tRNA synthetases, I think that ATP binding is crucial for all the work that needs to be done, since it is the energy source of the cell, so it is needed right at the beginning.
  • Expression Time References and Description: I made my own hypothesis by taking conclusions from the protein's functionality.

Gene Context

  • Other Components: thrS
  • Possible Dependencies: L-histidine
  • Process: histidyl-tRNA aminoacylation
    • Inputs: ATP, L-histidine, tRNA(His)
    • Outputs: AMP, diphosphate, L-histidyl-tRNA(His)
  • Reference: F4MPL9

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