Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.89 kDa 
• Atom Count: 4,354 
• Modelled Residue Count: 435 
• Deposited Residue Count: 456 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 2DET

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state

• PDB DOI:  https://doi.org/10.2210/pdb2DET/pdb
• NDB: PR0193

• Classification: Transferase/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-17 Released: 2006-08-15 
• Deposition Author(s): Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.305 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 

Literature

Snapshots of tRNA sulphuration via an adenylated intermediate

Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

(2006) Nature 442: 419-424

• PubMed: 16871210 
• DOI: https://doi.org/10.1038/nature04896
• Primary Citation of Related Structures:  
  2DER, 2DET, 2DEU


• PubMed Abstract: 
  

Uridine at the first anticodon position (U34) of glutamate, lysine and glutamine transfer RNAs is universally modified by thiouridylase into 2-thiouridine (s2U34), which is crucial for precise translation by restricting codon-anticodon wobble during protein synthesis on the ribosome. However, it remains unclear how the enzyme incorporates reactive sulphur into the correct position of the uridine base. Here we present the crystal structures of the MnmA thiouridylase-tRNA complex in three discrete forms, which provide snapshots of the sequential chemical reactions during RNA sulphuration. On enzyme activation, an alpha-helix overhanging the active site is restructured into an idiosyncratic beta-hairpin-containing loop, which packs the flipped-out U34 deeply into the catalytic pocket and triggers the activation of the catalytic cysteine residues. The adenylated RNA intermediate is trapped. Thus, the active closed-conformation of the complex ensures accurate sulphur incorporation into the activated uridine carbon by forming a catalytic chamber to prevent solvent from accessing the catalytic site. The structures of the complex with glutamate tRNA further reveal how MnmA specifically recognizes its three different tRNA substrates. These findings provide the structural basis for a general mechanism whereby an enzyme incorporates a reactive atom at a precise position in a biological molecule.

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Organizational Affiliation: 

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-specific 2-thiouridylase mnmA	B [auth A]	380	Escherichia coli	Mutation(s): 0  EC: 2.8.1 (PDB Primary Data), 2.8.1.13 (UniProt)
UniProt
Find proteins for P25745 (Escherichia coli (strain K12)) Explore P25745  Go to UniProtKB:  P25745

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA	A [auth C]	76	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.305 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.537	α = 90
b = 108.015	β = 90
c = 211.239	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance