3GRU

Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.

O'Farrell, H.C.Musayev, F.N.Scarsdale, J.N.Rife, J.P.

(2010) Biochemistry 49: 2697-2704

  • DOI: 10.1021/bi901875x
  • Primary Citation of Related Structures:  
    3GRV, 3GRY, 3GRR, 3GRU

  • PubMed Abstract: 
  • The KsgA/Dim1 family of proteins is intimately involved in ribosome biogenesis in all organisms. These enzymes share the common function of dimethylating two adenosine residues near the 3'-OH end of the small subunit rRNA; orthologs in the three kingdoms, along with eukaryotic organelles, have evolved additional functions in rRNA processing, ribosome assembly, and, surprisingly, transcription in mitochondria ...

    The KsgA/Dim1 family of proteins is intimately involved in ribosome biogenesis in all organisms. These enzymes share the common function of dimethylating two adenosine residues near the 3'-OH end of the small subunit rRNA; orthologs in the three kingdoms, along with eukaryotic organelles, have evolved additional functions in rRNA processing, ribosome assembly, and, surprisingly, transcription in mitochondria. The methyltransferase reaction is intriguingly elaborate. The enzymes can bind to naked small subunit rRNA but cannot methylate their target bases until a subset of ribosomal proteins have bound and the nascent subunit has reached a certain level of maturity. Once this threshold is reached, the enzyme must stabilize two adenosines into the active site at separate times and two methyl groups must be transferred to each adenosine, with concomitant exchanges of the product S-adenosyl-l-homocysteine and the methyl donor substrate S-adenosyl-l-methionine. A detailed molecular understanding of this mechanism is currently lacking. Structural analysis of the interactions between the enzyme and substrate will aid in this understanding. Here we present the structure of KsgA from Methanocaldococcus jannaschii in complex with several ligands, including the first structure of S-adenosyl-l-methionine bound to a KsgA/Dim1 enzyme in a catalytically productive way. We also discuss the inability thus far to determine a structure of a target adenosine bound in its active site.


    Related Citations: 
    • Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli
      O'Farrell, H.C., Scarsdale, J.N., Rife, J.P.
      (2004) J Mol Biol 339: 337

    Organizational Affiliation

    Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia 23298-0133, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dimethyladenosine transferase A295Methanocaldococcus jannaschiiMutation(s): 2 
Gene Names: ksgAMJ1029
EC: 2.1.1
Find proteins for Q58435 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58435 
Go to UniProtKB:  Q58435
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.528α = 90
b = 66.276β = 107.52
c = 62.008γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary