1l0r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (18:47, 29 November 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1l0r.gif|left|200px]]
 
-
{{Structure
+
==NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins==
-
|PDB= 1l0r |SIZE=350|CAPTION= <scene name='initialview01'>1l0r</scene>
+
<StructureSection load='1l0r' size='340' side='right'caption='[[1l0r]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=NGP:NOGALAMYCIN (PROTONATED FORM)'>NGP</scene>
+
<table><tr><td colspan='2'>[[1l0r]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L0R FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NGP:NOGALAMYCIN+(PROTONATED+FORM)'>NGP</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l0r OCA], [https://pdbe.org/1l0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l0r RCSB], [https://www.ebi.ac.uk/pdbsum/1l0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l0r ProSAT]</span></td></tr>
-
 
+
</table>
-
'''NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins'''
+
<div style="background-color:#fffaf0;">
-
 
+
== Publication Abstract from PubMed ==
-
 
+
-
==Overview==
+
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized by a 5'-GAA loop, have been used to design novel intramolecular double hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3' and 5' terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites in intact duplex sequences, with pi-stacking interactions probably the single dominant stabilizing interaction.
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized by a 5'-GAA loop, have been used to design novel intramolecular double hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3' and 5' terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites in intact duplex sequences, with pi-stacking interactions probably the single dominant stabilizing interaction.
-
==About this Structure==
+
Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins.,Williams HE, Colgrave ML, Searle MS Eur J Biochem. 2002 Mar;269(6):1726-33. PMID:11895443<ref>PMID:11895443</ref>
-
1L0R 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=1L0R OCA].
+
-
 
+
-
==Reference==
+
-
Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins., Williams HE, Colgrave ML, Searle MS, Eur J Biochem. 2002 Mar;269(6):1726-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11895443 11895443]
+
-
[[Category: Protein complex]]
+
-
[[Category: Colgrave, M L.]]
+
-
[[Category: Searle, M S.]]
+
-
[[Category: Williams, H E.L.]]
+
-
[[Category: NA]]
+
-
[[Category: NGP]]
+
-
[[Category: drug-dna recognition]]
+
-
[[Category: gaa loop]]
+
-
[[Category: nogalamycin intercalation]]
+
-
[[Category: single strand break]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:24:45 2008''
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1l0r" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Colgrave ML]]
 +
[[Category: Searle MS]]
 +
[[Category: Williams HEL]]

Current revision

NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins

PDB ID 1l0r

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l0r"
Personal tools