Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase F
Synonym: TTHA1387
GI: 55981356
COG: COG0144
UniProt: Q5SII2
Structures: | 3M6U | 3M6V | 3M6W | 3M6X |
Alpha Fold Predicted Structure: AF-Q5SII2-F1
Enzyme type: methyltransferase
Position of modification - modification: s:1378(1400) - m5C
s:1382(1404) - m5C
s:1385(1407) - m5C


PDB Structures:


3M6U

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Cells devote a significant effort toward the production of multiple modified nucleotides in rRNAs, which fine tune the ribosome function. Here, we report that two methyltransferases, RsmB and RsmF, are responsible for all four 5-methylcytidine (m(5)C) modifications in 16S rRNA of Thermus thermophilus. Like Escherichia coli RsmB, T. thermophilus RsmB produces m(5)C967. In contrast to E. coli RsmF, which introduces a single m(5)C1407 modification, T. thermophilus RsmF modifies three positions, generating m(5)C1400 and m(5)C1404 in addition to m(5)C1407. These three residues are clustered near the decoding site of the ribosome, but are situated in distinct structural contexts, suggesting a requirement for flexibility in the RsmF active site that is absent from the E. coli enzyme. Two of these residues, C1400 and C1404, are sufficiently buried in the mature ribosome structure so as to require extensive unfolding of the rRNA to be accessible to RsmF. In vitro, T. thermophilus RsmF methylates C1400, C1404, and C1407 in a 30S subunit substrate, but only C1400 and C1404 when naked 16S rRNA is the substrate. The multispecificity of T. thermophilus RsmF is potentially explained by three crystal structures of the enzyme in a complex with cofactor S-adenosyl-methionine at up to 1.3 A resolution. In addition to confirming the overall structural similarity to E. coli RsmF, these structures also reveal that key segments in the active site are likely to be dynamic in solution, thereby expanding substrate recognition by T. thermophilus RsmF.

Download RCSB-PDB Structures:

Pdb Files   3M6U.pdb   3M6V.pdb   3M6W.pdb   3M6X.pdb  
Pdbx/mmCIF Files   3M6U.cif   3M6V.cif   3M6W.cif   3M6X.cif  


Protein sequence:

MLPKAFLSRMAELLGEEFPAFLKALTEGKRTYGLRVNTLKLPPEAFQRISPWPLRPIPWCQEGFYYPEEARPGPHPFFYAGLYYIQEPSAQAVGVLLDPKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALAEAFGTYFHRVLLDAPCSGEGMFRKDREAARHWGPSAPKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAHPEFRLEDARLHPLFAPGVPEWGEGNPELLKTARLWPHRLEGEGHFLARFRKEGGAWSTPRLERPSPLSQEALRAFRGFLEEAGLTLEGPVLDRAGHLYLLPEGLPTLLGLKAPAPGLYLGKVQKGRFLPARALALAFGATLPWPEGLPRLALTPEDPRALAFATGEGVAWEGEDHPLALVVLKTAAGEFPLDFGKAKRGVLRPVGVGL

Comments:

At variance with E. coli site-specific RsmF, which introduces a single m5C1407 modification, the T. thermophilus ortholog is a multisite-specific methyltransferase that modifies three positions, generating m5C1400, m5C1404 and m5C1407 in the 16S rRNA of a 30S subunit substrate. When naked 16S rRNA is tested as substrate, only C1400 and C1404 can be methylated in vitro. These residues, C1400 and C1404, are sufficiently buried in the mature ribosome structure so as to require extensive unfolding of the rRNA to be accessible to RsmF. Moreover, comparison of structures of E. coli and T. thermophilus RsmF reveals that key segments in the active site are likely to be dynamic in solution, thereby expanding substrate recognition by T. thermophilus RsmF




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m5C RNA rRNA 1400 SSU-16S Prokaryotic Cytosol 20558545   
C:m5C RNA rRNA 1404 SSU-16S Prokaryotic Cytosol 20558545   
C:m5C RNA rRNA 1386 SSU-16S Prokaryotic Cytosol 20558545   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M L P K A F L S R M A E L L G E E F P A F L K A L T E G K R T Y G L R V N T L K L P P E A F Q R I S P W P L R P I P W C Q E G F Y Y P E E A R P G P H P F F Y A G L Y Y I Q E P S A Q A V G V L L D P K P G E R V L D L A A A P G G K T T H L A A R M G G K G L L L A N E V D G K R V R G L L E N V E R W G A P L A V T Q A P P R A L A E A F G T Y F H R V L L D A P C S G E G M F R K D R E A A R H W G P S A P K R M A E V Q K A L L A Q A S R L L G P G G V L V Y S T C T F A P E E N E G V V A H F L K A H P E F R L E D A R L H P L F A P G V P E W G E G N P E L L K T A R L W P H R L E G E G H F L A R F R K E G G A W S T P R L E R P S P L S Q E A L R A F R G F L E E A G L T L E G P V L D R A G H L Y L L P E G L P T L L G L K A P A P G L Y L G K V Q K G R F L P A R A L A L A F G A T L P W P E G L P R L A L T P E D P R A L A F A T G E G V A W E G E D H P L A L V V L K T A A G E F P L D F G K A K R G V L R P V G V G L

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q5SII2-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SII2-F1.cif  
DSSP Secondary Structures   Q5SII2.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G RNA [details] 20558545 -