1sn8
From Proteopedia
(New page: 200px<br /><applet load="1sn8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sn8, resolution 2.00Å" /> '''Crystal structure of...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1sn8.jpg|left|200px]]<br /><applet load="1sn8" size=" | + | [[Image:1sn8.jpg|left|200px]]<br /><applet load="1sn8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1sn8, resolution 2.00Å" /> | caption="1sn8, resolution 2.00Å" /> | ||
'''Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)'''<br /> | '''Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | S1 domains occur in four of the major enzymes of mRNA decay in Escherichia | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1SN8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PB as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1SN8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=PB:'>PB</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SN8 OCA]. |
==Reference== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Cook, M | + | [[Category: Cook, M A.]] |
| - | [[Category: Edge, R | + | [[Category: Edge, R E.]] |
[[Category: Lario, P.]] | [[Category: Lario, P.]] | ||
| - | [[Category: Mackie, G | + | [[Category: Mackie, G A.]] |
| - | [[Category: McIntosh, L | + | [[Category: McIntosh, L P.]] |
[[Category: Schubert, M.]] | [[Category: Schubert, M.]] | ||
| - | [[Category: Strynadka, N | + | [[Category: Strynadka, N C.J.]] |
[[Category: PB]] | [[Category: PB]] | ||
[[Category: ob-fold]] | [[Category: ob-fold]] | ||
[[Category: rna-binding]] | [[Category: rna-binding]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:03:15 2008'' |
Revision as of 13:03, 21 February 2008
|
Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)
Overview
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.
About this Structure
1SN8 is a Single protein structure of sequence from Escherichia coli with as ligand. Full crystallographic information is available from OCA.
Reference
Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces., Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP, J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:15312761
Page seeded by OCA on Thu Feb 21 15:03:15 2008
