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Crystal Structure of A. aeolicus TrmH/SpoU tRNA modifying enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus.

Pleshe, E.Truesdell, J.Batey, R.T.

(2005) Acta Crystallogr.,Sect.F 61: 722-728

  • DOI: 10.1107/S1744309105022980

  • PubMed Abstract: 
  • Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar ...

    Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of S-adenosylmethionine (SAM) dependent methyltransferases. In bacteria, many of these modifications in tRNA and rRNA are carried out by the alpha/beta-knot superfamily of enzymes, whose SAM-binding pocket is created by a characteristic deep trefoil knot. TrmH, an enzyme found throughout all three kingdoms of life, modifies the universally conserved guanosine 18 position of tRNA. The crystal structure of TrmH from the thermophilic bacterium Aquifex aeolicus has been determined at 1.85 A resolution using data collected from a synchrotron-radiation source. The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the alpha/beta-knot superfamily, with alpha-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Campus Box 215, Boulder, CO 80309-0215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (Guanosine-2'-O-)-methyltransferase
A
211Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: trmH (spoU)
EC: 2.1.1.34
Find proteins for O67577 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67577
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.658α = 90.00
b = 66.658β = 90.00
c = 194.884γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance