The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.
BACKGROUND
. The translation elongation factor EF-Tu in its GTP-bound state forms a ternary complex with any aminoacylated tRNA (aa-tRNA), except initiator tRNA and selenocysteinyl-tRNA. This complex delivers aa-tRNA to the ribosomal A site during the elongation cycle of translation. The crystal structure of the yeast Phe-tRNAPhe ternary complex with Thermus aquaticus EF-Tu-GDPNP (Phe-TC) has previously been determined as one representative of this general yet highly discriminating complex formation.


RESULTS
The ternary complex of Escherichia coli Cys-tRNACys and T. aquaticus EF-Tu-GDPNP (Cys-TC) has been solved and refined at 2.6 degrees resolution. Conserved and variable features of the aa-tRNA recognition and binding by EF-Tu-GTP have been revealed by comparison with the Phe-TC structure. New tertiary interactions are observed in the tRNACys structure. A 'kissing complex' is observed in the very close crystal packing arrangement.


CONCLUSIONS
The recognition of Cys-tRNACys by EF-Tu-GDPNP is restricted to the aa-tRNA motif previously identified in Phe-TC and consists of the aminoacylated 3' end, the phosphorylated 5' end and one side of the acceptor stem and T stem. The aminoacyl bond is recognized somewhat differently, yet by the same primary motif in EF-Tu, which suggests that EF-Tu adapts to subtle variations in this moiety among all aa-tRNAs. New tertiary interactions revealed by the Cys-tRNACys structure, such as a protonated C16:C59 pyrimidine pair, a G15:G48 'Levitt pair' and an s4U8:A14:A46 base triple add to the generic understanding of tRNA structure from sequence. The structure of the 'kissing complex' shows a quasicontinuous helix with a distinct shape determined by the number of base pairs.
Nissen
P
P
Institute of Molecular and Structural Biology, Aarhus University, Gustav Wieds Vej 10, C DK 8000 Aarhus C, Denmark.
Thirup
S
S
Kjeldgaard
M
M
Nyborg
J
J
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry; D020963:GTP Phosphohydrolase-Linked Elongation Factors / Q000737:chemistry; D006160:Guanosine Triphosphate / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010444:Peptide Elongation Factor Tu / Q000737:chemistry*; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D012350:RNA, Transfer, Cys / Q000737:chemistry*; D012360:RNA, Transfer, Phe / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry; D016415:Sequence Alignment; D013824:Thermus / Q000737:chemistry*
D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012350:RNA, Transfer, Cys; D012360:RNA, Transfer, Phe; D016601:RNA-Binding Proteins; D006160:Guanosine Triphosphate; D020963:GTP Phosphohydrolase-Linked Elongation Factors; D010444:Peptide Elongation Factor Tu