1esy
From Proteopedia
(New page: 200px<br /> <applet load="1esy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1esy" /> '''NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1esy.gif|left|200px]]<br /> | + | [[Image:1esy.gif|left|200px]]<br /><applet load="1esy" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="1esy" size=" | + | |
caption="1esy" /> | caption="1esy" /> | ||
'''NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM'''<br /> | '''NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The genome of the human immunodeficiency virus type-1 (HIV-1) contains a | + | The genome of the human immunodeficiency virus type-1 (HIV-1) contains a stretch of approximately 120 nucleotides known as the psi-site that is essential for RNA packaging during virus assembly. These nucleotides have been proposed to form four stem-loops (SL1-SL4) that have both independent and overlapping functions. Stem-loop SL2 is important for efficient recognition and packaging of the full-length, unspliced viral genome, and also contains the major splice-donor site (SD) for mRNA splicing. We have determined the structure of the 19-residue SL2 oligoribonucleotide by heteronuclear NMR methods. The structure is generally consistent with the most recent of two earlier secondary structure predictions, with residues G1-G2-C3-G4 and C6-U7 forming standard Watson Crick base-pairs with self-complementary residues C16-G17-C18-C19 and A12-G13, respectively. However, residue A15, which is located near the center of the stem, does not form a predicted bulge, and residues A5 and U14 do not form an expected Watson-Crick base-pair. Instead, these residues form a novel A5-U14-A15 base-triple that appears to be stabilized by hydrogen bonds from A15-H61 and -H62 to A5-N1 and U14-O2, respectively; from A5-H61 to U14-O2, and from C16-H42 to U14-O2'. A kink in the backbone allows the aromatic rings of the sequential U14-A15 residues to be approximately co-planar, adopting a stable "platform motif" that is structurally similar to the A-A (adenosine) platforms observed in the P4-P6 ribozyme domain of the Tetrahymena group I intron. Platform motifs generally function in RNA by mediating long-range interactions, and it is therefore possible that the A-U-A base-triple platform mediates long-range interactions that either stabilize the psi-RNA or facilitate splicing and/or packaging. Residue G8 of the G8-G9-U10-G11 tetraloop is stacked above the U7-A12 base-pair, and the remaining tetraloop residues are disordered and available for potential interactions with either other RNA or protein components. |
==About this Structure== | ==About this Structure== | ||
| - | 1ESY 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:// | + | 1ESY 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=1ESY OCA]. |
==Reference== | ==Reference== | ||
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform., Amarasinghe GK, De Guzman RN, Turner RB, Summers MF, J Mol Biol. 2000 May 26;299(1):145-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860728 10860728] | NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform., Amarasinghe GK, De Guzman RN, Turner RB, Summers MF, J Mol Biol. 2000 May 26;299(1):145-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860728 10860728] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Amarasinghe, G | + | [[Category: Amarasinghe, G K.]] |
| - | [[Category: Guzman, R | + | [[Category: Guzman, R N.De.]] |
| - | [[Category: Summers, M | + | [[Category: Summers, M F.]] |
| - | [[Category: Turner, R | + | [[Category: Turner, R B.]] |
[[Category: hiv-1]] | [[Category: hiv-1]] | ||
[[Category: nmr structure]] | [[Category: nmr structure]] | ||
| Line 23: | Line 22: | ||
[[Category: splice-donor site]] | [[Category: splice-donor site]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:31:10 2008'' |
Revision as of 10:31, 21 February 2008
|
NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM
Overview
The genome of the human immunodeficiency virus type-1 (HIV-1) contains a stretch of approximately 120 nucleotides known as the psi-site that is essential for RNA packaging during virus assembly. These nucleotides have been proposed to form four stem-loops (SL1-SL4) that have both independent and overlapping functions. Stem-loop SL2 is important for efficient recognition and packaging of the full-length, unspliced viral genome, and also contains the major splice-donor site (SD) for mRNA splicing. We have determined the structure of the 19-residue SL2 oligoribonucleotide by heteronuclear NMR methods. The structure is generally consistent with the most recent of two earlier secondary structure predictions, with residues G1-G2-C3-G4 and C6-U7 forming standard Watson Crick base-pairs with self-complementary residues C16-G17-C18-C19 and A12-G13, respectively. However, residue A15, which is located near the center of the stem, does not form a predicted bulge, and residues A5 and U14 do not form an expected Watson-Crick base-pair. Instead, these residues form a novel A5-U14-A15 base-triple that appears to be stabilized by hydrogen bonds from A15-H61 and -H62 to A5-N1 and U14-O2, respectively; from A5-H61 to U14-O2, and from C16-H42 to U14-O2'. A kink in the backbone allows the aromatic rings of the sequential U14-A15 residues to be approximately co-planar, adopting a stable "platform motif" that is structurally similar to the A-A (adenosine) platforms observed in the P4-P6 ribozyme domain of the Tetrahymena group I intron. Platform motifs generally function in RNA by mediating long-range interactions, and it is therefore possible that the A-U-A base-triple platform mediates long-range interactions that either stabilize the psi-RNA or facilitate splicing and/or packaging. Residue G8 of the G8-G9-U10-G11 tetraloop is stacked above the U7-A12 base-pair, and the remaining tetraloop residues are disordered and available for potential interactions with either other RNA or protein components.
About this Structure
1ESY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform., Amarasinghe GK, De Guzman RN, Turner RB, Summers MF, J Mol Biol. 2000 May 26;299(1):145-56. PMID:10860728
Page seeded by OCA on Thu Feb 21 12:31:10 2008
