1foy: Difference between revisions

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THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE

OverviewOverview

The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.

About this StructureAbout this Structure

1FOY is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.

ReferenceReference

The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA., Hinck AP, Markus MA, Huang S, Grzesiek S, Kustonovich I, Draper DE, Torchia DA, J Mol Biol. 1997 Nov 21;274(1):101-13. PMID:9398519

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OCA

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-[[Image:1foy.gif|left|200px]]<br /><applet load="1foy" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1foy.gif|left|200px]]<br /><applet load="1foy" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1foy" />
 '''THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE'''<br />
 ==Overview==
-The three-dimensional solution structure has been determined by NMR, spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11, (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to, a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose, secondary structure consists of three helical stems and a central junction, loop. The NMR data reveal that the conserved structural core of the, protein, which consists of a bundle of three alpha-helices and a, two-stranded parallel beta-sheet four residues in length, is nearly the, same as the solution structure determined for the non-liganded form of the, protein. There are however, substantial chemical shift perturbations which, accompany RNA binding, the largest of which map onto an extended loop, which bridges the C-terminal end of alpha-helix 1 and the first strand of, parallel beta-sheet. Substantial shift perturbations are also observed in, the N-terminal end of alpha-helix 1, the intervening loop that bridges, helices 2 and 3, and alpha-helix 3. The four contact regions identified by, the shift perturbation data also displayed protein-RNA NOEs, as identified, by isotope-filtered three-dimensional NOE spectroscopy. The shift, perturbation and NOE data not only implicate helix 3 as playing an, important role in RNA binding, but also indicate that regions flanking, helix 3 are involved as well. Loop 1 is of particular interest as it was, found to be flexible and disordered for L11-C76 free in solution, but not, in the RNA-bound form of the protein, where it appears rigid and adopts a, specific conformation as a result of its direct contact to RNA.
+The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.
 ==About this Structure==
-FOY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FOY OCA].
+FOY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FOY OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Geobacillus stearothermophilus]]
 [[Category: Single protein]]
-[[Category: Draper, D.E.]]
+[[Category: Draper, D E.]]
 [[Category: Grzesiek, S.]]
-[[Category: Hinck, A.P.]]
+[[Category: Hinck, A P.]]
 [[Category: Huang, S.]]
 [[Category: Kustanovich, I.]]
-[[Category: Markus, M.A.]]
+[[Category: Markus, M A.]]
-[[Category: Torchia, D.A.]]
+[[Category: Torchia, D A.]]
 [[Category: protein/rna]]
 [[Category: ribosome]]
 [[Category: thiostrepton]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:06:23 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:40:59 2008''