The structure of the TrmE GTP-binding protein and its implications for tRNA modification.
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.
Scrima
Andrea
A
Max-Planck Institut für Molekulare Physiologie, Dortmund, Germany.
Vetter
Ingrid R
IR
Armengod
M Eugenia
ME
Wittinghofer
Alfred
A
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D019204:GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006153:Guanosine Diphosphate / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012343:RNA, Transfer / Q000378:metabolism*; D016415:Sequence Alignment; D013763:Tetrahydrofolates / Q000378:metabolism; D014529:Uridine / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; C417279:TRME protein, Thermotoga maritima; D013763:Tetrahydrofolates; D006153:Guanosine Diphosphate; C030371:5,6,7,8-tetrahydrofolic acid; D006160:Guanosine Triphosphate; D012343:RNA, Transfer; D019204:GTP-Binding Proteins; D014529:Uridine