1sn8
From Proteopedia
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|PDB= 1sn8 |SIZE=350|CAPTION= <scene name='initialview01'>1sn8</scene>, resolution 2.00Å | |PDB= 1sn8 |SIZE=350|CAPTION= <scene name='initialview01'>1sn8</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PB:LEAD (II) ION'>PB</scene> | + | |LIGAND= <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1slj|1SLJ]], [[1smx|1SMX]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sn8 OCA], [http://www.ebi.ac.uk/pdbsum/1sn8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1sn8 RCSB]</span> | ||
}} | }} | ||
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[[Category: Schubert, M.]] | [[Category: Schubert, M.]] | ||
[[Category: Strynadka, N C.J.]] | [[Category: Strynadka, N C.J.]] | ||
| - | [[Category: PB]] | ||
[[Category: ob-fold]] | [[Category: ob-fold]] | ||
[[Category: rna-binding]] | [[Category: rna-binding]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:44:24 2008'' |
Revision as of 20:44, 30 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | RNE, AMS, HMP1, B1084 (Escherichia coli) | ||||||
| Related: | 1SLJ, 1SMX
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
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