1sy4: Difference between revisions

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[[Image:1sy4.gif|left|200px]]<br /><applet load="1sy4" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1sy4.gif|left|200px]]<br /><applet load="1sy4" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1sy4" />

'''Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)'''<br />

==Overview==

Phosphorothioate-substitution experiments are often used to elucidate, functionally important metal ion-binding sites on RNA. All previous, experiments with S(P)-phosphorothioate-substituted RNAs have been done in, the absence of structural information for this particular diastereomer., Yeast U6 RNA contains a metal ion-binding site that is essential for, spliceosome function and includes the pro-S(P) oxygen 5' of U(80)., S(P)-phosphorothioate substitution at this location creates spliceosomes, dependent on thiophilic ions for the first step of splicing. We have, determined the solution structure of the U(80), S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and, also report the refined NMR structure of the unmodified U6 ISL. Both, structures were determined with inclusion of (1)H-(13)C residual dipolar, couplings. The precision of the structures with and without, phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison, of the local and long-range structural effect of the modification. We find, that the U6-ISL structure is unperturbed by the phosphorothioate., Additionally, the thermodynamic stability of the U6 ISL is dependent on, the protonation state of the A(79)-C(67) wobble pair and is not affected, by the adjacent phosphorothioate. These results indicate that a single, S(P)-phosphorothioate substitution can be structurally benign, and further, validate the metal ion rescue experiments used to identify the essential, metal-binding site(s) in the spliceosome.

Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer. Yeast U6 RNA contains a metal ion-binding site that is essential for spliceosome function and includes the pro-S(P) oxygen 5' of U(80). S(P)-phosphorothioate substitution at this location creates spliceosomes dependent on thiophilic ions for the first step of splicing. We have determined the solution structure of the U(80) S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and also report the refined NMR structure of the unmodified U6 ISL. Both structures were determined with inclusion of (1)H-(13)C residual dipolar couplings. The precision of the structures with and without phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison of the local and long-range structural effect of the modification. We find that the U6-ISL structure is unperturbed by the phosphorothioate. Additionally, the thermodynamic stability of the U6 ISL is dependent on the protonation state of the A(79)-C(67) wobble pair and is not affected by the adjacent phosphorothioate. These results indicate that a single S(P)-phosphorothioate substitution can be structurally benign, and further validate the metal ion rescue experiments used to identify the essential metal-binding site(s) in the spliceosome.

==About this Structure==

1SY4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure ~~superseeds~~ the now removed PDB entry 1NYZ. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA].

1SY4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure supersedes the now removed PDB entry 1NYZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA].

==Reference==

Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12702812 12702812]

[[Category: Protein complex]]

[[Category: Allman, A.M.]]

[[Category: Allman, A M.]]

[[Category: Butcher, S.E.]]

[[Category: Butcher, S E.]]

[[Category: Johnson, R.J.]]

[[Category: Johnson, R J.]]

[[Category: Nikstad, L.J.]]

[[Category: Nikstad, L J.]]

[[Category: Reiter, N.J.]]

[[Category: Reiter, N J.]]

[[Category: a-c wobble pair]]

[[Category: internal loop]]

Line 22:

[[Category: stem-loop (gnra-like tetraloop)]]

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@@ Line 1: / Line 1: @@
-[[Image:1sy4.gif|left|200px]]<br /><applet load="1sy4" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1sy4.gif|left|200px]]<br /><applet load="1sy4" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1sy4" />
 '''Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)'''<br />
 ==Overview==
-Phosphorothioate-substitution experiments are often used to elucidate, functionally important metal ion-binding sites on RNA. All previous, experiments with S(P)-phosphorothioate-substituted RNAs have been done in, the absence of structural information for this particular diastereomer., Yeast U6 RNA contains a metal ion-binding site that is essential for, spliceosome function and includes the pro-S(P) oxygen 5' of U(80)., S(P)-phosphorothioate substitution at this location creates spliceosomes, dependent on thiophilic ions for the first step of splicing. We have, determined the solution structure of the U(80), S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and, also report the refined NMR structure of the unmodified U6 ISL. Both, structures were determined with inclusion of (1)H-(13)C residual dipolar, couplings. The precision of the structures with and without, phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison, of the local and long-range structural effect of the modification. We find, that the U6-ISL structure is unperturbed by the phosphorothioate., Additionally, the thermodynamic stability of the U6 ISL is dependent on, the protonation state of the A(79)-C(67) wobble pair and is not affected, by the adjacent phosphorothioate. These results indicate that a single, S(P)-phosphorothioate substitution can be structurally benign, and further, validate the metal ion rescue experiments used to identify the essential, metal-binding site(s) in the spliceosome.
+Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer. Yeast U6 RNA contains a metal ion-binding site that is essential for spliceosome function and includes the pro-S(P) oxygen 5' of U(80). S(P)-phosphorothioate substitution at this location creates spliceosomes dependent on thiophilic ions for the first step of splicing. We have determined the solution structure of the U(80) S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and also report the refined NMR structure of the unmodified U6 ISL. Both structures were determined with inclusion of (1)H-(13)C residual dipolar couplings. The precision of the structures with and without phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison of the local and long-range structural effect of the modification. We find that the U6-ISL structure is unperturbed by the phosphorothioate. Additionally, the thermodynamic stability of the U6 ISL is dependent on the protonation state of the A(79)-C(67) wobble pair and is not affected by the adjacent phosphorothioate. These results indicate that a single S(P)-phosphorothioate substitution can be structurally benign, and further validate the metal ion rescue experiments used to identify the essential metal-binding site(s) in the spliceosome.
 ==About this Structure==
-SY4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure superseeds the now removed PDB entry 1NYZ. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA].
+SY4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure supersedes the now removed PDB entry 1NYZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA].
 ==Reference==
 Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12702812 12702812]
 [[Category: Protein complex]]
-[[Category: Allman, A.M.]]
+[[Category: Allman, A M.]]
-[[Category: Butcher, S.E.]]
+[[Category: Butcher, S E.]]
-[[Category: Johnson, R.J.]]
+[[Category: Johnson, R J.]]
-[[Category: Nikstad, L.J.]]
+[[Category: Nikstad, L J.]]
-[[Category: Reiter, N.J.]]
+[[Category: Reiter, N J.]]
 [[Category: a-c wobble pair]]
 [[Category: internal loop]]
@@ Line 22: / Line 22: @@
 [[Category: stem-loop (gnra-like tetraloop)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:17:45 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:06:58 2008''