17ra
From Proteopedia
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'''BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES''' | '''BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=17RA OCA]. | |
==Reference== | ==Reference== | ||
NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein., Smith JS, Nikonowicz EP, Biochemistry. 1998 Sep 29;37(39):13486-98. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9753434 9753434] | NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein., Smith JS, Nikonowicz EP, Biochemistry. 1998 Sep 29;37(39):13486-98. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9753434 9753434] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Nikonowicz, E P.]] | [[Category: Nikonowicz, E P.]] | ||
[[Category: Smith, J S.]] | [[Category: Smith, J S.]] | ||
| - | [[Category: | + | [[Category: Base triple]] |
| - | [[Category: | + | [[Category: Branchpoint helix]] |
| - | [[Category: | + | [[Category: Bulge]] |
| - | [[Category: | + | [[Category: Phage ms2]] |
| - | [[Category: | + | [[Category: Ribonucleic acid]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:33:49 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 06:33, 2 May 2008
BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES
Overview
The RNA molecules that make up the spliceosome branch-point helix and the binding site for phage GA coat protein share a secondary structure motif in which two consecutive adenine residues occupy the strand opposite a single uridine, creating the potential to form one of two different A.U base pairs while leaving the other adenine unpaired or bulged. During the splicing of introns out of pre-mRNA, the 2'-OH of the bulged adenine participates in the transesterification reaction at the 5'-exon and forms the branch-point residue of the lariat intermediate. Either adenine may act as the branch-point residue in mammals, but the 3'-proximal adenine does so preferentially. When bound to phage GA coat protein, the bulged adenine loops out of the helix and occupies a binding pocket on the surface of the protein, forming a nucleation complex for phage assembly. The coat protein can bind helices with bulged adenines at either position, but the 3'-proximal site binds with greater affinity. We have studied this RNA motif in a 21 nucleotide hairpin containing a GA coat protein-binding site whose four nucleotide loop has been replaced by a more stable loop from the related phage Ms2. Using heteronuclear NMR spectroscopy, we have determined the structure of this hairpin to an overall precision of 2.0 A. Both adenine bases stack into the helix, and while all available NOE and coupling constant data are consistent with both possible A.U base pairs, the base pair involving the 5'-proximal adenine appears to be the major conformation. The 3'-proximal bulged adenine protonates at unusually high pH, and to account for this, we propose a model in which the protonated adenine is stabilized by a hydrogen bond to the uridine O2 of the A.U base pair. The 2'-OH of the bulged adenine adopts a regular A-form helical geometry, suggesting that in order to participate in the splicing reaction, the conformation of the branch-point helix in the active spliceosome may change from the conformation described here. Thus, while the adenine site preferences of the spliceosome and of phage GA may be due to protein factors, the preferred adenine is predisposed in the free RNA to conformational rearrangement involved in formation of the active complexes.
About this Structure
Full crystallographic information is available from OCA.
Reference
NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein., Smith JS, Nikonowicz EP, Biochemistry. 1998 Sep 29;37(39):13486-98. PMID:9753434 Page seeded by OCA on Fri May 2 09:33:49 2008
