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 PQS (software)

Macromolecule Content

• Total Structure Weight: 47.32 kDa 
• Atom Count: 3037 
• Modelled Residue Count: 372 
• Deposited Residue Count: 413 
• Unique protein chains: 1

2C5S

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

• DOI: 10.2210/pdb2C5S/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-11-01 Released: 2005-11-30 
• Deposition Author(s): Waterman, D.G., Ortiz-Lombardia, M., Fogg, M.J., Koonin, E.V., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain.

Waterman, D.G., Ortiz-Lombardia, M., Fogg, M.J., Koonin, E.V., Antson, A.A.

(2006) J Mol Biol 356: 97-110

• PubMed: 16343540 
• DOI: 10.1016/j.jmb.2005.11.013
• Primary Citation of Related Structures:  
  2C5S


• PubMed Abstract: 
  

ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This base acts as a sensitive trigger for the response mechanism to UV exposure, providing protection against its damaging effects. We present the crystal structure of Bacillus anthracis ThiI in complex with AMP, revealing an extended tripartite architecture in which an N-terminal ferredoxin-like domain (NFLD) connects the C-terminal catalytic PP-loop pyrophosphatase domain with a THUMP domain, an ancient predicted RNA-binding domain that is widespread in all kingdoms of life. We describe the structure of the THUMP domain, which appears to be unrelated to RNA-binding domains of known structure. Mapping the conserved residues of NFLD and the THUMP domain onto the ThiI structure suggests that these domains jointly form the tRNA-binding surface. The inaccessibility of U8 in the canonical L-shaped form of tRNA, and the existence of a glycine-rich linker joining the catalytic and RNA-binding moieties of ThiI suggest that structural changes may occur in both molecules upon binding.

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Organizational Affiliation: 

York Structural Biology Laboratory, University of York, Chemistry Department, York YO10 5YW, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII	A	413	Bacillus anthracis str. Ames	Mutation(s): 0  EC: 2.8.1.4
Find proteins for Q81KU0 (Bacillus anthracis) Explore Q81KU0  Go to UniProtKB:  Q81KU0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	A	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.047	α = 90
b = 81.047	β = 90
c = 140.893	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-01 
• Released Date: 2005-11-30 
Deposition Author(s): Waterman, D.G., Ortiz-Lombardia, M., Fogg, M.J., Koonin, E.V., Antson, A.A.

Revision History  

• Version 1.0: 2005-11-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references, Other, Refinement description