Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.06 kDa 
• Atom Count: 6288 
• Modelled Residue Count: 728 
• Deposited Residue Count: 746 
• Unique protein chains: 1

3TM4

Crystal structure of Trm14 from Pyrococcus furiosus in complex with S-adenosylmethionine

• PDB DOI: 10.2210/pdb3TM4/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-31 Released: 2012-03-14 
• Deposition Author(s): Fislage, M., Roovers, M., Tuszynska, I., Bujnicki, J.M., Droogmans, L., Versees, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.

Fislage, M., Roovers, M., Tuszynska, I., Bujnicki, J.M., Droogmans, L., Versees, W.

(2012) Nucleic Acids Res 40: 5149-5161

• PubMed: 22362751 
• DOI: 10.1093/nar/gks163
• Primary Citation of Related Structures:  
  3TLJ, 3TM4, 3TM5, 3TMA


• PubMed Abstract: 
  

Methyltransferases (MTases) form a major class of tRNA-modifying enzymes needed for the proper functioning of tRNA. Recently, RNA MTases from the TrmN/Trm14 family that are present in Archaea, Bacteria and Eukaryota have been shown to specifically modify tRNA(Phe) at guanosine 6 in the tRNA acceptor stem. Here, we report the first X-ray crystal structures of the tRNA m(2)G6 (N(2)-methylguanosine) MTase (TTC)TrmN from Thermus thermophilus and its ortholog (Pf)Trm14 from Pyrococcus furiosus. Structures of (Pf)Trm14 were solved in complex with the methyl donor S-adenosyl-l-methionine (SAM or AdoMet), as well as the reaction product S-adenosyl-homocysteine (SAH or AdoHcy) and the inhibitor sinefungin. (TTC)TrmN and (Pf)Trm14 consist of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase (RFM) domain. These results represent the first crystallographic structure analysis of proteins containing both THUMP and RFM domain, and hence provide further insight in the contribution of the THUMP domain in tRNA recognition and catalysis. Electrostatics and conservation calculations suggest a main tRNA binding surface in a groove between the THUMP domain and the MTase domain. This is further supported by a docking model of TrmN in complex with tRNA(Phe) of T. thermophilus and via site-directed mutagenesis.

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Organizational Affiliation: 

VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine N2-)-methyltransferase Trm14	A, B	373	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF1002, trm14 EC: 2.1.1 (PDB Primary Data), 2.1.1.256 (UniProt)
UniProt
Find proteins for Q8U248 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U248  Go to UniProtKB:  Q8U248

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.08	α = 90
b = 45.17	β = 91.79
c = 121.43	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-31 
• Released Date: 2012-03-14 
Deposition Author(s): Fislage, M., Roovers, M., Tuszynska, I., Bujnicki, J.M., Droogmans, L., Versees, W.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Other
• Version 1.2: 2012-10-03
  Changes: Database references