Modomics - A Database of RNA Modifications

ID Card:

Full name: Probable ribosomal RNA small subunit methyltransferase
Synonym: TTHA0533
GI: 55980502
COG: COG2813
UniProt: Q5SKW0
Structures: | 3DMH | 3DMG | 3DMF | 2ZUL | 2ZWV |
Alpha Fold Predicted Structure: AF-Q5SKW0-F1
Enzyme type: methyltransferase predicted


PDB Structures:


3DMH

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Yet to be published

Download RCSB-PDB Structures:

Pdb Files   2ZUL.pdb   2ZWV.pdb   3DMG.pdb   3DMH.pdb   3MDF.pdb  
Pdbx/mmCIF Files   2ZUL.cif   2ZWV.cif   3DMG.cif   3DMH.cif   3MDF.cif  


Protein sequence:

MSLTREAYHRLTPLPHPGGRLFIKPGARGYRDPVHDLLQKTVEPFGERALDLNPGVGWGSLPLEGRMAVERLETSRAAFRCLTASGLQARLALPWEAAAGAYDLVVLALPAGRGTAYVQASLVAAARALRMGGRLYLAGDKNKGFERYFKEARALLGYGVVVRREGPYRVALLEKEKEAPPLPSLWRAFSARILGAEYTFHHLPGVFSAGKVDPASLLLLEALQERLGPEGVRGRQVLDLGAGYGALTLPLARMGAEVVGVEDDLASVLSLQKGLEANALKAQALHSDVDEALTEEARFDIIVTNPPFHVGGAVILDVAQAFVNVAAARLRPGGVFFLVSNPFLKYEPLLEEKFGAFQTLKVAEYKVLFAEKRGR

Comments:

RsmC catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to G1207 (E. coli numbering) in helix 34 of 16S rRNA (m2G1207). The enzyme is composed of two homologous domains tandemly duplicated within a single polypeptide. The crystal structure reveals that the orientation of target nucleotide in the active site reveals that G1207 has to disengage from its Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out into the active site prior to its modification. This is consistent with previous hypothesis that this enzyme recognizes a subunit assembly intermediate, not the free 16S rRNA, nor the fully mature 30S-subunit ribosome. T. thermophilus RsmC is closely related to E. coli RsmC and E. coli RsmD (m2G966/16S rRNA) as well as to other MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB)





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q5SKW0-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SKW0-F1.cif  
DSSP Secondary Structures   Q5SKW0.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. Tscherne JS, Nurse K, Popienick P, Ofengand J J Biol Chem [details] 9873033 -
Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. Demirci H, Gregory ST, Dahlberg AE, Jogl G J Biol Chem [details] 18667428 -

Links:

_PubMed_