Modomics - A Database of RNA Modifications

ID Card:

Full name: RNA small subunit Methyltransferase A
Synonym: ksgA
GI: 2632309
COG: COG0030
UniProt: P37468
Structures: | 6IFS | 6IFT | 6IFV | 6IFW | 7V2L | 7V2M | 7V2N | 7V2O | 7V2P | 7V2Q |
Alpha Fold Predicted Structure: AF-P37468-F1
Enzyme type: methyltransferase predicted


PDB Structures:


6IFS

Structure Description:

Title: KsgA from Bacillus subtilis 168
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.27
R value free: 0.238
R value observed: 0.179
R value work: 0.177

Abstract of the PDB Structure's related Publication:

Post-translational methylation of rRNA at select positions is a prevalent resistance mechanism adopted by pathogens. In this work, KsgA, a housekeeping ribosomal methyltransferase (rMtase) involved in ribosome biogenesis, was exploited as a model system to delineate the specific targeting determinants that impart substrate specificity to rMtases. With a combination of evolutionary and structure-guided approaches, a set of chimeras were created that altered the targeting specificity of KsgA such that it acted similarly to erythromycin-resistant methyltransferases (Erms), rMtases found in multidrug-resistant pathogens. The results revealed that specific loop embellishments on the basic Rossmann fold are key determinants in the selection of the cognate RNA. Moreover, in vivo studies confirmed that chimeric constructs are competent in imparting macrolide resistance. This work explores the factors that govern the emergence of resistance and paves the way for the design of specific inhibitors useful in reversing antibiotic resistance.

Download RCSB-PDB Structures:

Pdb Files   6IFS.pdb   6IFT.pdb   6IFV.pdb   6IFW.pdb   7V2L.pdb   7V2M.pdb   7V2N.pdb   7V2O.pdb   7V2P.pdb   7V2Q.pdb  
Pdbx/mmCIF Files   6IFS.cif   6IFT.cif   6IFV.cif   6IFW.cif   7V2L.cif   7V2M.cif   7V2N.cif   7V2O.cif   7V2P.cif   7V2Q.cif  


Protein sequence:

MNKDIATPIRTKEILKKYGFSFKKSLGQNFLIDTNILNRIVDHAEVTEKTGVIEIGPGIGALTEQLAKRAKKVVAFEIDQRLLPILKDTLSPYENVTVIHQDVLKADVKSVIEEQFQDCDEIMVVANLPYYVTTPIIMKLLEEHLPLKGIVVMLQKEVAERMAADPSSKEYGSLSIAVQFYTEAKTVMIVPKTVFVPQPNVDSAVIRLILRDGPAVDVENESFFFQLIKASFAQRRKTLLNNLVNNLPEGKAQKSTIEQVLEETNIDGKRRGESLSIEEFAALSNGLYKALF

Comments:

RsmA (formerly KsgA) dimethylates two very conserved adjacent adenosines (positions 1518 and 1519 in E. coli numbering) in the loop of a conserved hairpin h45 near the 3'-end of 16S rRNA. AdoMet is the methyl group donor. Mutation in ksgA gene confers a modest level of resistance to kasugamycin. RsmA belongs to the erm family of methyltransferases responsible for certain antibiotic resistance.





Alpha Fold Predicted Structure:




Parsing response... [271007/271007]


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Protein sequence:

M N K D I A T P I R T K E I L K K Y G F S F K K S L G Q N F L I D T N I L N R I V D H A E V T E K T G V I E I G P G I G A L T E Q L A K R A K K V V A F E I D Q R L L P I L K D T L S P Y E N V T V I H Q D V L K A D V K S V I E E Q F Q D C D E I M V V A N L P Y Y V T T P I I M K L L E E H L P L K G I V V M L Q K E V A E R M A A D P S S K E Y G S L S I A V Q F Y T E A K T V M I V P K T V F V P Q P N V D S A V I R L I L R D G P A V D V E N E S F F F Q L I K A S F A Q R R K T L L N N L V N N L P E G K A Q K S T I E Q V L E E T N I D G K R R G E S L S I E E F A A L S N G L Y K A L F
50100150200250SequenceGHTSN

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-P37468-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P37468-F1.cif  
DSSP Secondary Structures   P37468.dssp  





Publications:

Links:

_PubMed_