Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 59.41 kDa 
• Atom Count: 2663 
• Modelled Residue Count: 304 
• Deposited Residue Count: 510 
• Unique protein chains: 1

4CNG

Crystal structure of Sulfolobus acidocaldarius TrmJ in complex with S-adenosyl-L-Homocysteine

• PDB DOI: 10.2210/pdb4CNG/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfolobus acidocaldarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-01-22 Released: 2014-07-02 
• Deposition Author(s): Van Laer, B., Somme, J., Roovers, M., Steyaert, J., Droogmans, L., Versees, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.

Somme, J., Van Laer, B., Roovers, M., Steyaert, J., Versees, W., Droogmans, L.

(2014) RNA 20: 1257

• PubMed: 24951554 
• DOI: 10.1261/rna.044503.114
• Primary Citation of Related Structures:  
  4CND, 4CNE, 4CNF, 4CNG


• PubMed Abstract: 
  

The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2'-O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level.

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Organizational Affiliation: 

Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPOU RRNA METHYLASE	A, B	255	Sulfolobus acidocaldarius	Mutation(s): 1  EC: 2.1.1.200 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for Q4JB16 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4JB16  Go to UniProtKB:  Q4JB16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], D [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.185 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.803	α = 90
b = 54.097	β = 90
c = 130.637	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-22 
• Released Date: 2014-07-02 
Deposition Author(s): Van Laer, B., Somme, J., Roovers, M., Steyaert, J., Droogmans, L., Versees, W.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references