The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
The structure of the complex between ribosomal protein L25 and a 37 nucleotide RNA molecule, which contains the E-loop and helix IV regions of the E-domain of Escherichia coli 5S rRNA, has been determined to an overall r.m.s. displacement of 1.08 A (backbone heavy atoms) by heteronuclear NMR spectroscopy (Protein Databank code 1d6k). The interacting molecular surfaces are bipartite for both the RNA and the protein. One side of the six-stranded beta-barrel of L25 recognizes the minor groove of the E-loop with very little change in the conformations of either the protein or the RNA and with the RNA-protein interactions occurring mainly along one strand of the E-loop duplex. This minor groove recognition module includes two parallel beta-strands of L25, a hitherto unknown RNA binding topology. Binding of the RNA also induces conversion of a flexible loop to an alpha-helix in L25, the N-terminal tip of which interacts with the widened major groove at the E-loop/helix IV junction of the RNA. The structure of the complex reveals that the E-domain RNA serves as a preformed docking partner, while the L25 protein has one preformed and one induced recognition module.
Stoldt
M
M
Abteilung Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie, Postfach 100813, 07708 Jena, Germany.
Wöhnert
J
J
Ohlenschläger
O
O
Görlach
M
M
Brown
L R
LR
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000378:metabolism
D012329:RNA, Bacterial; D012341:RNA, Ribosomal, 5S; D012269:Ribosomal Proteins; C031127:ribosomal protein L25