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==Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain== | |||
<StructureSection load='5hlt' size='340' side='right'caption='[[5hlt]], [[Resolution|resolution]] 2.67Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5hlt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_pumilus Bacillus pumilus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HLT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HLT FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.672Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YPE:4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL+DIHYDROGEN+PHOSPHATE'>YPE</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=5hlt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hlt OCA], [https://pdbe.org/5hlt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hlt RCSB], [https://www.ebi.ac.uk/pdbsum/5hlt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hlt ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A3FMN7_BACPU A3FMN7_BACPU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 A resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic pi-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores. | |||
Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.,Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R Nucleic Acids Res. 2016 Sep 6;44(15):7079-89. doi: 10.1093/nar/gkw644. Epub 2016 , Jul 15. PMID:27422870<ref>PMID:27422870</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5hlt" style="background-color:#fffaf0;"></div> | ||
[[Category: Aeschimann | |||
[[Category: Haener | ==See Also== | ||
[[Category: | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus pumilus]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Aeschimann W]] | |||
[[Category: Chau T-T-H]] | |||
[[Category: Haener R]] | |||
[[Category: Langenegger SM]] | |||
[[Category: Probst M]] | |||
[[Category: Stocker A]] | |||
Latest revision as of 13:46, 16 August 2023
Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domainCrystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
Structural highlights
FunctionPublication Abstract from PubMedThe use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 A resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic pi-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.,Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R Nucleic Acids Res. 2016 Sep 6;44(15):7079-89. doi: 10.1093/nar/gkw644. Epub 2016 , Jul 15. PMID:27422870[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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