Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase D
Synonym: Rv2966c
GI: 15610103
COG: COG0742
UniProt: P95128
Structures: | 3P9N |
Alpha Fold Predicted Structure: AF-P95128-F1
Enzyme type: methyltransferase


PDB Structures:


3P9N

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Nine of ten methylated nucleotides of Escherichia coli 16 S rRNA are conserved in Mycobacterium tuberculosis. All the 10 different methyltransferases are known in E. coli, whereas only TlyA and GidB have been identified in mycobacteria. Here we have identified Rv2966c of M. tuberculosis as an ortholog of RsmD protein of E. coli. We have shown that rv2966c can complement rsmD-deleted E. coli cells. Recombinant Rv2966c can use 30 S ribosomes purified from rsmD-deleted E. coli as substrate and methylate G966 of 16 S rRNA in vitro. Structure determination of the protein shows the protein to be a two-domain structure with a short hairpin domain at the N terminus and a C-terminal domain with the S-adenosylmethionine-MT-fold. We show that the N-terminal hairpin is a minimalist functional domain that helps Rv2966c in target recognition. Deletion of the N-terminal domain prevents binding to nucleic acid substrates, and the truncated protein fails to carry out the m(2)G966 methylation on 16 S rRNA. The N-terminal domain also binds DNA efficiently, a property that may be utilized under specific conditions of cellular growth.

Download RCSB-PDB Structures:

Pdb Files   3P9N.pdb  
Pdbx/mmCIF Files   3P9N.cif  


Protein sequence:

MTRIIGGVAGGRRIAVPPRGTRPTTDRVRESLFNIVTARRDLTGLAVLDLYAGSGALGLEALSRGAASVLFVESDQRSAAVIARNIEALGLSGATLRRGAVAAVVAAGTTSPVDLVLADPPYNVDSADVDAILAALGTNGWTREGTVAVVERATTCAPLTWPEGWRRWPQRVYGDTRLELAERLFANV

Comments:

As its E. coli ortholog, M. tuberculosis RsmB uses 30S ribosomes as substrate and methylates G966 in the loop of hairpin 31 of 16S rRNA in vitro. Structure determination of the enzyme shows the protein to be a two-domain structure with a short hairpin domain at the N terminus and a C-terminal domain with the S-adenosylmethionine-MT-Rossmann fold. RsmD and RsmC (catalyzing formation of m2G207) both posses a common MTase domain in the C-terminus (Rossmann-fold) and a variable region in the N-terminus that is related to the YbiN family of MTases (formation of m6A1618 by RlmF). This N-terminal hairpin is a minimalist functional domain that helps Rv2966c in target recognition.





Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P95128-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P95128-F1.cif  
DSSP Secondary Structures   P95128.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural and functional characterization of Rv2966c protein reveals an RsmD-like methyltransferase from Mycobacterium tuberculosis and the role of its N-terminal domain in target recognition. Kumar A, Saigal K, Malhotra K, Sinha KM, Taneja B J Biol Chem [details] 21474448 -