PDBsum entry 3fyd

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protein ligands links
Transferase PDB id
Protein chain
263 a.a. *
SO4 ×5
Waters ×333
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of dim1 from the thermophilic archeon, methanocaldococcus jannaschi
Structure: Probable dimethyladenosine transferase. Chain: a. Synonym: s-adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase, 16s rrna dimethylase. Engineered: yes. Mutation: yes
Source: Methanocaldococcus jannaschii. Methanococcus jannaschii. Organism_taxid: 2190. Gene: ksga, mj1029. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.75Å     R-factor:   0.181     R-free:   0.226
Authors: J.N.Scarsdale,F.N.Musayev,J.P.Rife
Key ref:
N.Pulicherla et al. (2009). Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J Mol Biol, 391, 884-893. PubMed id: 19520088 DOI: 10.1016/j.jmb.2009.06.015
22-Jan-09     Release date:   30-Jun-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q58435  (RSMA_METJA) -  Probable ribosomal RNA small subunit methyltransferase A
275 a.a.
263 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     methylation   4 terms 
  Biochemical function     transferase activity     6 terms  


DOI no: 10.1016/j.jmb.2009.06.015 J Mol Biol 391:884-893 (2009)
PubMed id: 19520088  
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
N.Pulicherla, L.A.Pogorzala, Z.Xu, H.C.O Farrell, F.N.Musayev, J.N.Scarsdale, E.A.Sia, G.M.Culver, J.P.Rife.
The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point, no examples of archaeal structures have been reported. Here, we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here, we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of temperatures.
  Selected figure(s)  
Figure 1.
Fig. 1. Representative 2F[o] − F[c] electron density map, contoured to 1.0 σ, of both forms of MjDim1. Shown are the side chains from select residues. (a) Form 1. (b) Form 2.
Figure 2.
Fig. 2. Structure of MjDim1. (a) Two views, rotated 180°, of the structure of MjDim1. α-Helices are in cyan and β-strands are in magenta. The orange broken line separates the two domains. The linker connecting the two domains is labeled, as are the domains. (b) A close-up of the N-terminal domain highlighting the ligand binding pockets, as annotated.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 391, 884-893) copyright 2009.  
  Figures were selected by an automated process.