1SLJ

Solution structure of the S1 domain of RNase E from E. coli

1SLJ の概要

• エントリーDOI: 10.2210/pdb1slj/pdb
• 関連するPDBエントリー: 1smx 1sn8
• NMR情報: BMRB: 6122
• 分子名称: Ribonuclease E (1 entity in total)
• 機能のキーワード: ob-fold, rna-binding, hydrolase
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm: P21513
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 10704.13

構造登録者

Schubert, M.,Edge, R.E.,Lario, P.,Cook, M.A.,Strynadka, N.C.J.,Mackie, G.A.,McIntosh, L.P. (登録日: 2004-03-05, 公開日: 2004-08-17, 最終更新日: 2024-05-22)

主引用文献

Schubert, M.,Edge, R.E.,Lario, P.,Cook, M.A.,Strynadka, N.C.,Mackie, G.A.,McIntosh, L.P.
Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.
J.Mol.Biol., 341:37-54, 2004

PubMed Abstract: S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.

PubMed: 15312761
DOI: 10.1016/j.jmb.2004.05.061

実験手法

SOLUTION NMR