1exl
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1exl |SIZE=350|CAPTION= <scene name='initialview01'>1exl</scene> | |PDB= 1exl |SIZE=350|CAPTION= <scene name='initialview01'>1exl</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=2AR:2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE'>2AR</scene>, <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=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=1exl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exl OCA], [http://www.ebi.ac.uk/pdbsum/1exl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1exl RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: modified nucleotide]] | [[Category: modified nucleotide]] | ||
| - | ''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 20:11:36 2008'' |
Revision as of 17:11, 30 March 2008
| |||||||
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN
Overview
2'-deoxyaristeromycin (dAr) is a nucleoside analogue that is resistant to the action of DNA glycosylases. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of an 11-mer DNA containing a single dAr.T base pair at its center. Analysis of the spectra revealed the existence of a right-handed duplex in solution, stabilized by Watson-Crick hydrogen bonding and base-stacking interactions. The carbocyclic sugar adopted a C1'-exo conformation and sugars of the 3'-flanking base pair had puckers in the O4'-endo range. The dAr.T base pair was mildly propeller twisted, and the dAr analogue showed a positive roll with the 3'-flanking base. Our findings indicate that the observed resistance of dAr-containing oligodeoxynucleotides to the catalytic action of DNA glycosylases relates to its electronic properties rather than structure, and validate the use of dAr and related carbocyclic nucleoside analogues for biological and structure/function relationship studies.
About this Structure
1EXL is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of an 11-mer DNA duplex containing the carbocyclic nucleotide analog: 2'-deoxyaristeromycin., Smirnov S, Johnson F, Marumoto R, de los Santos C, J Biomol Struct Dyn. 2000 Jun;17(6):981-91. PMID:10949165
Page seeded by OCA on Sun Mar 30 20:11:36 2008
