This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2dd2
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2dd2 |SIZE=350|CAPTION= <scene name='initialview01'>2dd2</scene> | |PDB= 2dd2 |SIZE=350|CAPTION= <scene name='initialview01'>2dd2</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=PR5:PURINE+RIBOSIDE-5'-MONOPHOSPHATE'>PR5</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2dd1|2DD1]], [[2dd3|2DD3]], [[1xv0|1XV0]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd2 OCA], [http://www.ebi.ac.uk/pdbsum/2dd2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dd2 RCSB]</span> | ||
}} | }} | ||
| Line 35: | Line 38: | ||
[[Category: thermodynamic]] | [[Category: thermodynamic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:33:03 2008'' |
Revision as of 23:33, 30 March 2008
| |||||||
| Ligands: | , , , , | ||||||
| Related: | 2DD1, 2DD3, 1XV0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack
Overview
A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.
About this Structure
2DD2 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425
Page seeded by OCA on Mon Mar 31 02:33:03 2008
