Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase B
Synonym: YjfH, JW4138
GI: 52783780
Orf: b4180
COG: COG0566
UniProt: P63177
Structures: | 1GZ0 |
Alpha Fold Predicted Structure: AF-P63177-F1
Enzyme type: methyltransferase
Position of modification - modification: l:2251(2251) - Gm


PDB Structures:


1GZ0

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

In Escherichia coli, RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. The crystal structure of this 2'O-methyltransferase has been determined at 2.5 A resolution. RlmB consists of an N-terminal domain connected by a flexible extended linker to a catalytic C-terminal domain and forms a dimer in solution. The C-terminal domain displays a divergent methyltransferase fold with a unique knotted region, and lacks the classic AdoMet binding site features. The N-terminal domain is similar to ribosomal proteins L7 and L30, suggesting a role in 23S rRNA recognition. The conserved residues in this novel family of 2'O-methyltransferases cluster in the knotted region, suggesting the location of the catalytic and AdoMet binding sites.

Download RCSB-PDB Structures:

Pdb Files   1GZ0.pdb  
Pdbx/mmCIF Files   1GZ0.cif  


Protein sequence:

MSEMIYGIHAVQALLERAPERFQEVFILKGREDKRLLPLIHALESQGVVIQLANRQYLDEKSDGAVHQGIIARVKPGRQYQENDLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQRS

Comments:

RlmB is a SPOUT-type of methyltransferase catalyzing formation of Gm at the conserved position 2251 in the peptidyltransferase domain V of large subunit rRNA (hairpin 80, also named P-loop). The ortholog SPOUT enzyme in S. cerevisiae is Mrm1 (formerly Pet56) catalyzing Gm at equivalent position 2270 (S. cerevisiae numbering) in large subunit mitochondrial rRNA. In cytoplasmic rRNA, the same conserved Gm is catalyzed at position 2619 (S. cerevisiae numbering) by C/D box RNP, guided by snR67. AdoMet is the donor of methyl group. The N-terminal domain of E. coli RlmB is similar to those in ribosomal proteins L7 and L30.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:Gm RNA rRNA 2251 LSU-23S Prokaryotic Cytosol 11698387   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P63177-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P63177-F1.cif  
DSSP Secondary Structures   P63177.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Michel G, Sauve V, Larocque R, Li Y, Matte A, Cygler M Structure [details] 12377117 -
The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli. Lovgren JM, Wikstrom PM J Bacteriol [details] 11698387 -