Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase A
Synonym: KsgA, JW0050
GI: 125699
Orf: b0051
COG: COG0030
UniProt: P06992
Structures: | 1QYR | 3TPZ | 4ADV |
Alpha Fold Predicted Structure: AF-P06992-F1
Enzyme type: methyltransferase
Position of modification - modification: s:1518(1518) - m6,6A
s:1519(1519) - m6,6A


PDB Structures:


1QYR

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The bacterial enzyme KsgA catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaebacteria, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In yeast, and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. Another ortholog has been discovered recently, h-mtTFB in human mitochondria, which has a second function; this enzyme is a nuclear-encoded mitochondrial transcription factor. The KsgA enzymes are homologous to another family of RNA methyltransferases, the Erm enzymes, which methylate a single adenosine base in 23S rRNA and confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. We have crystallized KsgA from Escherichia coli and solved its structure to a resolution of 2.1A. The structure bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to sc-mtTFB, the Saccharomyces cerevisiae version of h-mtTFB. Comparison of the three crystal structures and further study of the KsgA protein will provide insight into this interesting group of enzymes.

Download RCSB-PDB Structures:

Pdb Files   1QYR.pdb   3TPZ.pdb   4ADV.pdb  
Pdbx/mmCIF Files   1QYR.cif   3TPZ.cif   4ADV.cif  


Protein sequence:

MNNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENAPLQES

Comments:

RsmA (formerly KsgA) dimethylates two very conserved adjacent adenosines (positions 1518 and 1519) in the loop of a conserved hairpin h45 near the 3′-end of 16S rRNA. RsmA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis dual function). AdoMet is the methyl group donor. RsmA (Dim1p) is the yeast ortholog. They belong to the erm family of methyltransferase responsible for erythromycin resistance. Notice, the acronym RsmA has also been used for for Regulator of Secondary Metabolism A, a protein not related to the RNA small subunit Methyltransferase. Structure of the E. coli methyltransferase RsmA bound to the E. coli 30S ribosomal subunit was solved (4ADV).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m6A RNA rRNA 1518 SSU-16S 3'm-domain Prokaryotic Cytosol 21142019   
m6A:m6,6A RNA rRNA 1518 SSU-16S 3'm-domain Prokaryotic Cytosol 21142019   
A:m6A RNA rRNA 1519 SSU-16S 3'm-domain Prokaryotic Cytosol 21142019   
m6A:m6,6A RNA rRNA 1519 SSU-16S 3'm-domain Prokaryotic Cytosol 21142019   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M N N R V H Q G H L A R K R F G Q N F L N D Q F V I D S I V S A I N P Q K G Q A M V E I G P G L A A L T E P V G E R L D Q L T V I E L D R D L A A R L Q T H P F L G P K L T I Y Q Q D A M T F N F G E L A E K M G Q P L R V F G N L P Y N I S T P L M F H L F S Y T D A I A D M H F M L Q K E V V N R L V A G P N S K A Y G R L S V M A Q Y Y C N V I P V L E V P P S A F T P P P K V D S A V V R L V P H A T M P H P V K D V R V L S R I T T E A F N Q R R K T I R N S L G N L F S V E V L T G M G I D P A M R A E N I S V A Q Y C Q M A N Y L A E N A P L Q E 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-P06992-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P06992-F1.cif  
DSSP Secondary Structures   P06992.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. Boehringer D, O'Farrell HC, Rife JP, Ban N J Biol Chem [details] 22308031 -
Site-directed mutants of 16S rRNA reveal important RNA domains for KsgA function and 30S subunit assembly. Desai PM, Culver GM, Rife JP Biochemistry [details] 21142019 -
Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA. Connolly K, Rife JP, Culver G Mol Microbiol [details] 18990185 -
Control of substrate specificity by a single active site residue of the KsgA methyltransferase. O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP Biochemistry [details] 22142337 -
Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. Poldermans B, Roza L, Van Knippenberg PH J Biol Chem [details] 383712 -
Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16S ribosomal RNA of Escherichia coli. IV. The effect of the methylgroups on ribosomal subunit interaction. Poldermans B, Bakker H, Van Knippenberg PH Nucleic Acids Res [details] 6986611 -
Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. O'Farrell HC, Scarsdale JN, Rife JP J Mol Biol [details] 15136037 -