Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 22.71 kDa 
• Atom Count: 1757 
• Residue Count: 194 
• Unique protein chains: 1

1V2X

TrmH

• DOI: 10.2210/pdb1V2X/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2003-10-17 Released: 2004-05-04 
• Deposition Author(s): Nureki, O., Watanabe, K., Fukai, S., Ishii, R., Endo, Y., Hori, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Literature

Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme

Nureki, O., Watanabe, K., Fukai, S., Ishii, R., Endo, Y., Hori, H., Yokoyama, S.

(2004) Structure 12: 593-602

• PubMed: 15062082 
• DOI: 10.1016/j.str.2004.03.003
• Primary Citation of Related Structures:  
  1V2X


• PubMed Abstract: 
  

The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.

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Organizational Affiliation: 

Department of Biotechnology, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Gm18) methyltransferase	A	194	Thermus thermophilus	Mutation(s): 0  EC: 2.1.1.34
Find proteins for Q5SM16 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore Q5SM16  Go to UniProtKB:  Q5SM16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	A	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.601	α = 90
b = 44.023	β = 120.78
c = 56.756	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-17 
• Released Date: 2004-05-04 
Deposition Author(s): Nureki, O., Watanabe, K., Fukai, S., Ishii, R., Endo, Y., Hori, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2013-06-26
  Changes: Derived calculations