1SMX

Crystal structure of the S1 domain of RNase E from E. coli (native)

Summary for 1SMX

• Entry DOI: 10.2210/pdb1smx/pdb
• Related: 1SLJ 1SN8
• NMR Information: BMRB: 6122
• Descriptor: Ribonuclease E (2 entities in total)
• Functional Keywords: ob-fold, rna-binding, hydrolase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P21513
• Total number of polymer chains: 2
• Total formula weight: 21408.27

Authors

Schubert, M.,Edge, R.E.,Lario, P.,Cook, M.A.,Strynadka, N.C.J.,Mackie, G.A.,McIntosh, L.P. (deposition date: 2004-03-09, release date: 2004-08-17, Last modification date: 2024-04-03)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.8 Å)