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1fv8
From Proteopedia
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|PDB= 1fv8 |SIZE=350|CAPTION= <scene name='initialview01'>1fv8</scene> | |PDB= 1fv8 |SIZE=350|CAPTION= <scene name='initialview01'>1fv8</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DRT:2'-DEOXY-L-RIBO-FURANOSYL+THYMINE-5'-MONOPHOSPHATE'>DRT</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fv8 OCA], [http://www.ebi.ac.uk/pdbsum/1fv8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fv8 RCSB]</span> | ||
}} | }} | ||
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[[Category: heterochiral loop]] | [[Category: heterochiral loop]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:30:55 2008'' |
Revision as of 17:31, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR STUDY OF AN HETEROCHIRAL HAIRPIN
Overview
We carried out a structural study of the DNA heterochiral strand d (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine ) replaces T (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs to a strong topoisomerase II DNA cleavage site and which has been shown to resolve into a hairpin structure with a stem formed by eight Waston-Crick base-pairs and a single residue loop closed by an A.C sheared base-pair. Although - AT(L)C-, like its parent -ATC-, folds into a hairpin structure at low and high DNA concentrations it displays a lower stability (Tm of 56 degrees C versus 58.5 degrees C). Several NMR features in -AT(L)C- account for the disruption of the A.C pairing in the loop and a weakening of the C.G base-pair stability at the stem-loop junction. For instance, the exchange of the loop imino protons with solvent is accelerated compared with the natural oligonucleotide -ATC-. The higher flexibility of the heterochiral loop is confirmed by the results of NMR restrained molecular dynamics. In the calculated final structures of -AT(L)C-, the T10(L) residue moves the A9 and C11 residues away, thus preventing the loop closure through a C.A sheared base-pair and the achievement of a good base-base or sugar-base stacking. Actually, most of the stabilizing interactions present in -ATC- are lost in the heterochiral - AT(L)C- explaining its weaker stability.
About this Structure
1FV8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop., El Amri C, Mauffret O, Santamariar F, Tevanian G, Rayner S, Fermandjian S, J Biomol Struct Dyn. 2001 Dec;19(3):459-70. PMID:11790144
Page seeded by OCA on Sun Mar 30 20:30:55 2008
