2C5S

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

Summary for 2C5S

• Entry DOI: 10.2210/pdb2c5s/pdb
• Descriptor: PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: rna-binding protein, rna binding protein, trna modification, 4-thiouridine synthase, ferredoxin-like domain, thump domain, pp-loop pyrophosphatase domain, thiamine biosynthesis
• Biological source: BACILLUS ANTHRACIS
• Total number of polymer chains: 1
• Total formula weight: 47315.43

Authors

Waterman, D.G.,Ortiz-Lombardia, M.,Fogg, M.J.,Koonin, E.V.,Antson, A.A. (deposition date: 2005-11-01, release date: 2005-11-30, Last modification date: 2024-05-08)

Primary citation

Waterman, D.G.,Ortiz-Lombardia, M.,Fogg, M.J.,Koonin, E.V.,Antson, A.A.
Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain.
J.Mol.Biol., 356:97-110, 2006

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.

PubMed: 16343540
DOI: 10.1016/j.jmb.2005.11.013

Experimental method

X-RAY DIFFRACTION (2.5 Å)