1hz2: Difference between revisions
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|PDB= 1hz2 |SIZE=350|CAPTION= <scene name='initialview01'>1hz2</scene> | |PDB= 1hz2 |SIZE=350|CAPTION= <scene name='initialview01'>1hz2</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= | |||
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hz2 OCA], [http://www.ebi.ac.uk/pdbsum/1hz2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1hz2 RCSB]</span> | |||
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[[Category: Tsarouhtsis, D.]] | [[Category: Tsarouhtsis, D.]] | ||
[[Category: Zegar, I S.]] | [[Category: Zegar, I S.]] | ||
[[Category: dna duplex]] | [[Category: dna duplex]] | ||
[[Category: interstrand crosslink]] | [[Category: 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 21:12:21 2008'' | ||
Revision as of 21:12, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION NMR STRUCTURE OF SELF-COMPLEMENTARY DUPLEX 5'-D(AGGCG*CCT)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*. MODEL OF A MALONDIALDEHYDE CROSSLINK
OverviewOverview
Malondialdehyde (MDA), a known mutagen and suspected carcinogen, is a product of lipid peroxidation and byproduct of eicosanoid biosynthesis. MDA can react with DNA to generate potentially mutagenic adducts on adenine, cytosine, and particularly guanine. In addition, repair-dependent frame shift mutations in a GCGCGC region of Salmonella typhimurium hisD3052 have been attributed to formation of interstrand cross-links (Mukai, F. H. and Goldstein, B. D. Science 1976, 191, 868--869). The cross-linked species is unstable and has never been characterized but has been postulated to be a bis-imino linkage between N(2) positions of guanines. An analogous linkage has now been investigated as a stable surrogate using the self-complementary oligodeoxynucleotide sequence 5'-d(AGGCG*CCT)(2,) in which G* represents guanines linked via a trimethylene chain between N(2) positions. The solution structure, obtained by NMR spectroscopy and molecular dynamics using a simulated annealing protocol, revealed the cross-link only minimally distorts duplex structure in the region of the cross-link. The tether is accommodated by partially unwinding the duplex at the lesion site to produce a bulge and tipping the guanine residues; the two guanines and the tether attain a nearly planar conformation. This distortion did not result in significant bending of the DNA, a result which was confirmed by gel electrophoresis studies of multimers of a 21-mer duplex containing the cross-link.
About this StructureAbout this Structure
1HZ2 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5'-(CpG) motif: model of a malondialdehyde cross-link., Dooley PA, Tsarouhtsis D, Korbel GA, Nechev LV, Shearer J, Zegar IS, Harris CM, Stone MP, Harris TM, J Am Chem Soc. 2001 Feb 28;123(8):1730-9. PMID:11456774
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