193d: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
New page: left|200px<br /><applet load="193d" size="450" color="white" frame="true" align="right" spinBox="true" caption="193d" /> '''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERC...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:193d.gif|left|200px]]<br /><applet load="193d" size="450" color="white" frame="true" align="right" spinBox="true"
caption="193d" />
'''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX'''<br />


==Overview==
==SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX==
The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical, structure related to the antibiotic echinomycin which is known to, bisintercalate into DNA. Common features among these antibiotics include, two heterocyclic aromatic ring systems propagating from a cross-bridged, cyclic octadepsipeptide scaffold. We report on the solution structure of, the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex), based on a combined NMR-molecular dynamics study including intensity-based, refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the, duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6, and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are, wedge-shaped and unwound, with significant unwinding also observed at the, (C4-C5).(C4-G5) step bracketed between the intercalation sites. The, cross-bridged cyclic octadepsipeptide is positioned in the minor groove, with the methyl groups on its Ala and NMe-MCp residues directed towards, and making van der Waals contacts with the minor groove edge of the, duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala, backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e, to Ala-CO) account for the sequence specificity associated with complex, formation. The solution structure of the QN-DNA oligomer complex, which, contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA, oligomer complex, which contains Hoogsteen base-pairs on either side of, the bisintercalation site.
<StructureSection load='193d' size='340' side='right'caption='[[193d]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[193d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces Streptomyces]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=193D FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 4 models</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CPC:2-METHYL-1-METHYLAMINO-CYCLOPROPANE+CARBOXYLIC+ACID'>CPC</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=HQU:3-HYDROXYQUINALDIC+ACID'>HQU</scene>, <scene name='pdbligand=NCY:N-METHYLCYSTEINE'>NCY</scene>, <scene name='pdbligand=NYB:N-METHYL-S-[(1R)-1-METHYLPROPYL]-L-CYSTEINE'>NYB</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=193d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=193d OCA], [https://pdbe.org/193d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=193d RCSB], [https://www.ebi.ac.uk/pdbsum/193d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=193d ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6 and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-C5).(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.


==About this Structure==
Solution structure of a quinomycin bisintercalator-DNA complex.,Chen H, Patel DJ J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:7853395<ref>PMID:7853395</ref>
193D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CH3 and NBU as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Solution structure of a quinomycin bisintercalator-DNA complex., Chen H, Patel DJ, J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7853395 7853395]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 193d" style="background-color:#fffaf0;"></div>
[[Category: Chen, H.]]
== References ==
[[Category: Patel, D.J.]]
<references/>
[[Category: CH3]]
__TOC__
[[Category: NBU]]
</StructureSection>
[[Category: dna]]
[[Category: Large Structures]]
[[Category: double helix]]
[[Category: Streptomyces]]
[[Category: nmr]]
[[Category: Chen H]]
[[Category: quinomycin]]
[[Category: Patel DJ]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:12:08 2007''

Latest revision as of 21:55, 26 March 2025

SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=193d&oldid=4318223"