1XZP

Structure of the GTP-binding protein TrmE from Thermotoga maritima

Summary for 1XZP

• Entry DOI: 10.2210/pdb1xzp/pdb
• Related: 1XZQ
• Descriptor: Probable tRNA modification GTPase trmE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: gtp-binding, thf-binding, trna-modification, hydrolase
• Biological source: Thermotoga maritima; More
• Cellular location: Cytoplasm (By similarity): Q9WYA4 Q9WYA4
• Total number of polymer chains: 2
• Total formula weight: 71164.61

Authors

Scrima, A.,Vetter, I.R.,Armengod, M.E.,Wittinghofer, A. (deposition date: 2004-11-12, release date: 2005-01-04, Last modification date: 2024-03-13)

Primary citation

Scrima, A.,Vetter, I.R.,Armengod, M.E.,Wittinghofer, A.
The structure of the TrmE GTP-binding protein and its implications for tRNA modification
Embo J., 24:23-33, 2005

PubMed Abstract: TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal alpha/beta domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.

PubMed: 15616586
DOI: 10.1038/sj.emboj.7600507

Experimental method

X-RAY DIFFRACTION (2.3 Å)