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,PQS (software)

Macromolecule Content

• Total Structure Weight: 31.21 kDa 
• Atom Count: 2229 
• Residue Count: 243 
• Unique protein chains: 1

1UAL

Crystal structure of tRNA(m1G37)methyltransferase: Insight into tRNA recognition

• DOI: 10.2210/pdb1UAL/pdb

• Classification: TRANSFERASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-11 Released: 2003-06-17 
• Deposition Author(s): Ahn, H.J., Kim, H.-W., Yoon, H.-J., Lee, B.I., Suh, S.W., Yang, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Crystal structure of tRNA(m(1)G37)methyltransferase: insights into tRNA recognition

Ahn, H.J., Kim, H.-W., Yoon, H.-J., Lee, B.I., Suh, S.W., Yang, J.K.

(2003) EMBO J 22: 2593-2603

• PubMed: 12773376 
• DOI: 10.1093/emboj/cdg269
• Structures With Same Primary Citation


• PubMed Abstract: 
  

tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. Here we report four crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy and phosphate, and as an apo form. This first structure of TrmD indicates that it functions as a dimer. It also suggests the binding mode of G(36)G(37) in the active site of TrmD and the catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows structural similarity to trp repressor. We propose a plausible model for the TrmD(2)-tRNA(2) complex, which provides insights into recognition of the general tRNA structure by TrmD.

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Organizational Affiliation: 

Structural Proteomics Laboratory, School of Chemistry and Molecular Engineering, Seoul National University, Seoul 151-742, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
tRNA (Guanine-N(1)-)-methyltransferase	A	274	Haemophilus influenzae	Mutation(s): 0  EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43912  Go to UniProtKB:  P43912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	A	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.688	α = 90
b = 93.688	β = 90
c = 177.667	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-11 
• Released Date: 2003-06-17 
Deposition Author(s): Ahn, H.J., Kim, H.-W., Yoon, H.-J., Lee, B.I., Suh, S.W., Yang, J.K.

Revision History 

• Version 1.0: 2003-06-17
  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