MMSYN1 0361

From BioE80 Boot
Jump to: navigation, search

Author Information

Joey McKenna 05930701 (mckenj)

Basic Information

  • ID: MMSYN1_0361
  • Name: rlmH
  • Organism: JCVI-Syn3.0
  • Description: RlmH is a methyltransferase that catalyzes the addition of a methyl group in the N3 position of the pseudouridine (Ψ) residue at nucleotide 1915 in 23S rRNA [Purta08, Ero08]. The enzyme requires the intact ribosome and the presence of pseudouridine at position 1915 in 23S rRNA for activity [Ero08, Ero10]. m3Ψ1915 is the only currently known methylated pseudouridine residue in bacterial RNAs.

Computational docking between RlmH and the ribosome shows contacts with both ribosomal subunits [Purta08], consistent with the requirement for intact ribosomes for in vitro activity [Ero08].

RlmH is a member of the SPOUT superfamily of methyltransferases [Anantharaman02, Tkaczuk07] and belongs to the α/β knot superfamily of proteins [Mallam07, Tkaczuk07]. Thermodynamic and kinetic analysis of folding of RlmH shows that the protein folds via a simple three-state sequential mechanism [Mallam07]. Folding may involve a slipknot intermediate [Sulkowska09]. The RlmH polypeptide chain has a trefoil knot conformation even in the denatured state [Mallam10]. Backbone NMR assignments for urea-denatured RlmH have been reported [Hsieh13]. RlmH is a dimer in solution [Purta06, Mallam07, Mallam10].

RlmH activity is influenced by the presence of specific nucleotides in stem-loop 69 (H69) surrounding Ψ1915 in 23S RNA [Leppik12].

An rlmH deletion mutant lacks the m3Ψ1915 modification [Purta08, Ero08] and has a slightly lower growth rate than wild type [Purta08].

RlmH: "rRNA large subunit methyltransferase H" [Purta08, Ero08] Reference

  • DNA Length: 468 bp
  • DNA sequence:

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

  • Amino Acid length: 155 amino acids
  • Amino Acid sequence:

MKIKIICFGKLDKKFYIEAFNDYFKRLEKYADIEIIELKEEINGELNKIKELNSDLLLNKLESYKDFEKVILDVNSKLISTENLVDLIQTNLNYKNAKILFVIGPSDGYSKKFLNFFNNKISLAKITLPHQLCRIVLIEQIYRVFKIIKNEKYHK

Function and Homologs

  • Product: Ribosomal RNA large subunit methyltransferase H
  • Closest homologous proteins:
    • Name: hypothetical protein [Mycoplasma mycoides], Max Score: 299/Query Cover: 100%/E-Value: 1e-102/Ident: 100%, WP_020862695.1
    • Name: 50S rRNA methyltransferase [Mycoplasma mycoides], Max Score: 298/Query Cover: 100%/E-Value: 5e-102/Ident: 99% WP_017697863.1
  • Equivalent E. coli / JCVI functional protein: EG11254

Expression

  • Expression Level: [low].
  • Expression Level Hypothesis: I think that this gene operates at low expression levels because it is only need for RNA processing which is a less intense process then others.
  • Expression Level References and Description: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: [early].
  • Expression Level Hypothesis: An rRNA methyltransferase would be needed in the earlier stages of the central dogma, after DNA replication in the transcription process, because it deals with RNA processing before it is translated into a protein.
  • Expression Time References and Description: Intuition

Gene Context

  • Other Components: MMSYN1_0517
  • Possible Dependencies: pseudouridine synthase activity
  • Process: pseudouridine synthesis
    • Inputs: RNA uridine
    • Outputs: RNA pseudouridine

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