1feq
From Proteopedia
(New page: 200px<br /><applet load="1feq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1feq" /> '''NMR SOLUTION STRUCTURE OF THE ANTICODON OF T...) |
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| - | [[Image:1feq.gif|left|200px]]<br /><applet load="1feq" size=" | + | [[Image:1feq.gif|left|200px]]<br /><applet load="1feq" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1feq" /> | caption="1feq" /> | ||
'''NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37'''<br /> | '''NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the human tRNA(Lys3) anticodon stem and loop domain | + | The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding. |
==About this Structure== | ==About this Structure== | ||
| - | 1FEQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1FEQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FEQ OCA]. |
==Reference== | ==Reference== | ||
Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A., Stuart JW, Gdaniec Z, Guenther R, Marszalek M, Sochacka E, Malkiewicz A, Agris PF, Biochemistry. 2000 Nov 7;39(44):13396-404. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11063577 11063577] | Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A., Stuart JW, Gdaniec Z, Guenther R, Marszalek M, Sochacka E, Malkiewicz A, Agris PF, Biochemistry. 2000 Nov 7;39(44):13396-404. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11063577 11063577] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Agris, P | + | [[Category: Agris, P F.]] |
[[Category: Gdaniec, Z.]] | [[Category: Gdaniec, Z.]] | ||
| - | [[Category: Guenther, R | + | [[Category: Guenther, R H.]] |
[[Category: Malkiewicz, A.]] | [[Category: Malkiewicz, A.]] | ||
[[Category: Marszalek, M.]] | [[Category: Marszalek, M.]] | ||
[[Category: Sochacka, E.]] | [[Category: Sochacka, E.]] | ||
| - | [[Category: Stuart, J | + | [[Category: Stuart, J W.]] |
[[Category: anticodon stem loop]] | [[Category: anticodon stem loop]] | ||
[[Category: rna hairpin]] | [[Category: rna hairpin]] | ||
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[[Category: trna domain]] | [[Category: trna domain]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:37:52 2008'' |
Revision as of 10:37, 21 February 2008
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NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37
Overview
The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding.
About this Structure
1FEQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A., Stuart JW, Gdaniec Z, Guenther R, Marszalek M, Sochacka E, Malkiewicz A, Agris PF, Biochemistry. 2000 Nov 7;39(44):13396-404. PMID:11063577
Page seeded by OCA on Thu Feb 21 12:37:52 2008
