1luh
From Proteopedia
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|PDB= 1luh |SIZE=350|CAPTION= <scene name='initialview01'>1luh</scene> | |PDB= 1luh |SIZE=350|CAPTION= <scene name='initialview01'>1luh</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=TME:PROPANE'>TME</scene> | + | |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=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TME:PROPANE'>TME</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1luh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1luh OCA], [http://www.ebi.ac.uk/pdbsum/1luh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1luh RCSB]</span> | ||
}} | }} | ||
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[[Category: Stone, M P.]] | [[Category: Stone, M P.]] | ||
[[Category: Zhang, M.]] | [[Category: Zhang, M.]] | ||
| - | [[Category: TME]] | ||
[[Category: dna duplex]] | [[Category: dna duplex]] | ||
[[Category: guanine n2-guanine n2 interstrand crosslink]] | [[Category: guanine n2-guanine n2 interstrand crosslink]] | ||
| - | ''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 22:07:32 2008'' |
Revision as of 19:07, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*
Overview
Malondialdehyde interstrand cross-links in DNA show strong preference for 5'-d(CpG) sequences. The cross-links are unstable and a trimethylene cross-link has been used as a surrogate for structural studies. A previous structural study of the 5'-d(CpG) cross-link in the sequence 5'-d(AGGCGCCT), where G is the modified nucleotide, by NMR spectroscopy and molecular dynamics using a simulated annealing protocol showed the guanine residues and the tether lay approximately in a plane such that the trimethylene tether and probably the malondialdehyde tether, as well, could be accommodated without major disruptions of duplex structure [Dooley et al. J. Am Chem. Soc. 2001, 123, 1730-1739]. The trimethylene cross-link has now been studied in a GpC motif using the reverse sequence. The structure lacks the planarity seen with the 5'-d(CpG) sequence and is skewed about the trimethylene cross-link. Melting studies indicate that the trimethylene cross-link is thermodynamically less stable in the GpC motif than in the 5-d(CpG). Furthermore, lack of planarity of the GpC cross-link precludes making an isosteric replacement of the trimethylene tether by malondialdehyde. A similar argument can be used to explain the 5'-d(CpG) preference for interchain cross-linking by acrolein.
About this Structure
1LUH is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5'-d(GpC) motif., Dooley PA, Zhang M, Korbel GA, Nechev LV, Harris CM, Stone MP, Harris TM, J Am Chem Soc. 2003 Jan 8;125(1):62-72. PMID:12515507
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