2hkc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
[[Image:2hkc.gif|left|200px]]
[[Image:2hkc.gif|left|200px]]
-
{{Structure
+
<!--
-
|PDB= 2hkc |SIZE=350|CAPTION= <scene name='initialview01'>2hkc</scene>
+
The line below this paragraph, containing "STRUCTURE_2hkc", creates the "Structure Box" on the page.
-
|SITE=
+
You may change the PDB parameter (which sets the PDB file loaded into the applet)
-
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=GIQ:3-METHYL-3H-IMIDAZO[4,5-F]QUINOLIN-2-AMINE'>GIQ</scene>
+
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-
|ACTIVITY=
+
or leave the SCENE parameter empty for the default display.
-
|GENE=
+
-->
-
|DOMAIN=
+
{{STRUCTURE_2hkc| PDB=2hkc | SCENE= }}
-
|RELATEDENTRY=[[2hkb|2HKB]]
+
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hkc OCA], [http://www.ebi.ac.uk/pdbsum/2hkc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hkc RCSB]</span>
+
-
}}
+
'''NMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC'''
'''NMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC'''
Line 19: Line 16:
==About this Structure==
==About this Structure==
-
2HKC is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HKC OCA].
+
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HKC OCA].
==Reference==
==Reference==
Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions., Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP, J Am Chem Soc. 2006 Aug 9;128(31):10085-95. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16881637 16881637]
Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions., Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP, J Am Chem Soc. 2006 Aug 9;128(31):10085-95. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16881637 16881637]
-
[[Category: Protein complex]]
 
[[Category: DeMuro, N E.]]
[[Category: DeMuro, N E.]]
[[Category: Elmquist, C E.]]
[[Category: Elmquist, C E.]]
Line 30: Line 26:
[[Category: Stover, J S.]]
[[Category: Stover, J S.]]
[[Category: Wang, F.]]
[[Category: Wang, F.]]
-
[[Category: adduct]]
+
[[Category: Adduct]]
-
[[Category: anneal]]
+
[[Category: Anneal]]
-
[[Category: cosy]]
+
[[Category: Cosy]]
-
[[Category: dna]]
+
[[Category: Dna]]
-
[[Category: hca]]
+
[[Category: Hca]]
-
[[Category: iq]]
+
[[Category: Iq]]
-
[[Category: nar1iq3]]
+
[[Category: Nar1iq3]]
-
[[Category: nmr structure]]
+
[[Category: Nmr structure]]
-
[[Category: noesy]]
+
[[Category: Noesy]]
-
[[Category: refinement]]
+
[[Category: Refinement]]
-
[[Category: rmd calculation]]
+
[[Category: Rmd calculation]]
-
 
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 06:23:34 2008''
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:31:32 2008''
+

Revision as of 03:23, 4 May 2008

Image:2hkc.gif

Template:STRUCTURE 2hkc

NMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC


Overview

The solution structure of the oligodeoxynucleotide 5'-d(CTCGGCXCCATC)-3'.5'-d(GATGGCGCCGAG)-3' containing the heterocyclic amine 8-[(3-methyl-3H-imidazo[4,5-f]quinolin-2-yl)amino]-2'-deoxyguanosine adduct (IQ) at the third guanine in the NarI restriction sequence, a hot spot for -2 bp frameshifts, is reported. Molecular dynamics calculations restrained by distances derived from 24 (1)H NOEs between IQ and DNA, and torsion angles derived from (3)J couplings, yielded ensembles of structures in which the adducted guanine was displaced into the major groove with its glycosyl torsion angle in the syn conformation. One proton of its exocyclic amine was approximately 2.8 A from an oxygen of the 5' phosphodiester linkage, suggesting formation of a hydrogen bond. The carcinogen-guanine linkage was defined by torsion angles alpha' [N9-C8-N(IQ)-C2(IQ)] of 159 +/- 7 degrees and beta' [C8-N(IQ)-C2(IQ)-N3(IQ)] of -23 +/- 8 degrees . The complementary cytosine was also displaced into the major groove. This allowed IQ to intercalate between the flanking C.G base pairs. The disruption of Watson-Crick hydrogen bonding was corroborated by chemical-shift perturbations for base aromatic protons in the complementary strand opposite to the modified guanine. Chemical-shift perturbations were also observed for (31)P resonances corresponding to phosphodiester linkages flanking the adduct. The results confirmed that IQ adopted a base-displaced intercalated conformation in this sequence context but did not corroborate the formation of a hydrogen bond between the IQ quinoline nitrogen and the complementary dC [Elmquist, C. E.; Stover, J. S.; Wang, Z.; Rizzo, C. J. J. Am. Chem. Soc. 2004, 126, 11189-11201].

About this Structure

Full crystallographic information is available from OCA.

Reference

Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions., Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP, J Am Chem Soc. 2006 Aug 9;128(31):10085-95. PMID:16881637 Page seeded by OCA on Sun May 4 06:23:34 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hkc"
Personal tools