MMSYN1 0201

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Author Information

Camila Camacho

Basic Information

  • ID: MMSYN1_0201
  • Name: pdf
  • Organism: JCVI-Syn3.0
  • Description: A peptide deformylase (PDF) is an enzyme that catalyzes the chemical reaction formyl-L-methionyl peptide + H2O -> formate + methionyl peptide. Thus, the two substrates of this enzyme are formyl-L-methionyl peptide and H2O, whereas its two products are formate and methionyl peptide. This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. It is a member of the zinc metalloprotease family, defining a new subfamily Meinnel95a, Meinnel96. Peptide deformylase releases the formyl group from the amino terminal methionine residue of most nascent proteins Neidhardt96, Meinnel95. It interacts directly with the ribosome at the ribosomal exit tunnel BingelErlenmeye08 and competes with methionine aminopeptidase for the same site Sandikci13. Protein synthesis proceeds after formylation of methionine by methionyl-tRNA formyl transferase (FMT) and transfer of the charged initiator f-met tRNA to the ribosome. In eubacteria, deformylation of nascent peptides is required for subsequent cleavage of initiating methionines by methionine aminopeptidase. PDF provides an attractive target for the development of novel antibacterial agents Yuan06. The enzyme was long thought to be absent from eukaryotic organisms, but genome sequences have revealed its presence even in Homo sapiens, where it appears to be an evolutionary remnant (and thus it remains an excellent drug target) Nguyen03. PDF is essential in E. coli Mazel94.
  • DNA Length: 600 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 200 amino acids.
  • Amino Acid sequence:

MDKSYLLQDQIPSNSWLVKDHKKEIIRTKSTKIIDPTNLSNDEELVLKKLIDFVTFSQDENNNNINNKDYLRPAVGLAAPQIGVNKDMFYVRFQLDNNKIEQYAMINTKLISTSTQIACLKNGEGCLSVDNDHLGFVPRHYKIVVQGYDWLTKQYLTLTLRNYQAIVFQHEMDHNIGVLYYDHINKADPLYKDNSWIIIE

Function and Homologs

  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Name: peptide deformylase [Mycoplasma mycoides]/Max score: 412/Query Cover: 100%/E-value: 7e-146/Ident: 100%/Accession: WP_020862573.1
    • Name: peptide deformylase [Mycoplasma capricolum]/Max score: 410/Query Cover: 100%/E-value: 6e-145/Ident: 99%/Accession: WP_011387094.1
    • Name: peptide deformylase [Mycoplasma leachii]/Max score: 402/Query Cover: 100%/E-value: 5e-142/Ident: 97%/Accession: WP_013447560.1
  • Equivalent E. coli functional protein: EG11440.

Expression

  • Expression Level: [Low].
  • Expression Level Hypothesis: This protein helps in translation, meaning it is probably relatively important to be abundant in the cell. The dataset shows that the expression level for def (a related gene) is low, meaning that peptide deformylase might not be an amino acid commonly used in this organism's proteins. Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation Erlenmeyer1. The first enzymatic factor that processes nascent chains is peptide deformylase so, in general, this gene should be expressed at relatively high abundance because it is an important part of protein synthesis.
  • Expression Level References and Description: M. genitalium model data: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: [Early].
  • Expression Level Hypothesis: Since pdf is the first enzymatic factor that processes nascent chains and is required for messenger-RNA-directed protein synthesis and translation, this gene should be required early, but not necessarily at the beginning.
  • Expression Time References and Description: Erlenmeyer1 peptide deformylase

Gene Context

  • Other Components in the functional module: The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase.
  • Possible Dependencies: PDF specifically binds to the 50S ribosomal subunit via its C-terminal helix. rplW encodes the 50S ribosomal protein L23.
  • Process: Protein synthesis
    • Inputs: formyl-L-methionyl peptide, H2O
    • Outputs: formate, methionyl peptide

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