8qpc
From Proteopedia
(Difference between revisions)
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<table><tr><td colspan='2'>[[8qpc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius] 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=8QPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QPC FirstGlance]. <br> | <table><tr><td colspan='2'>[[8qpc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius] 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=8QPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QPC 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]] 3.24Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.24Å</td></tr> | ||
| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=V4F:8-(aminomethyl)-4-(phosphonomethoxy)quinoline-2-carboxylic+acid'>V4F</scene>, <scene name='pdbligand=V53:8-azanyl-4-(phosphonomethoxy)quinoline-2-carboxylic+acid'>V53</scene>, <scene name='pdbligand=V5F:( | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=V4F:8-(aminomethyl)-4-(phosphonomethoxy)quinoline-2-carboxylic+acid'>V4F</scene>, <scene name='pdbligand=V53:8-azanyl-4-(phosphonomethoxy)quinoline-2-carboxylic+acid'>V53</scene>, <scene name='pdbligand=V5F:(2~{R})-2-(2-azanylphenoxy)propanoic+acid'>V5F</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=8qpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qpc OCA], [https://pdbe.org/8qpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qpc RCSB], [https://www.ebi.ac.uk/pdbsum/8qpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qpc ProSAT]</span></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=8qpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qpc OCA], [https://pdbe.org/8qpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qpc RCSB], [https://www.ebi.ac.uk/pdbsum/8qpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qpc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/DN7D_SULAC DN7D_SULAC] Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990] | [https://www.uniprot.org/uniprot/DN7D_SULAC DN7D_SULAC] Can constrain negative DNA supercoils. May be involved in maintaining the integrity of the genome at high temperature.[UniProtKB:P61990] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked. | ||
| + | |||
| + | DNA Mimic Foldamer Recognition of a Chromosomal Protein.,Deepak D, Wu J, Corvaglia V, Allmendinger L, Scheckenbach M, Tinnefeld P, Huc I Angew Chem Int Ed Engl. 2024 Dec 23:e202422958. doi: 10.1002/anie.202422958. PMID:39714421<ref>PMID:39714421</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 8qpc" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein
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