5tnu: Difference between revisions
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==S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution== | ==S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution== | ||
<StructureSection load='5tnu' size='340' side='right' caption='[[5tnu]], [[Resolution|resolution]] 3.05Å' scene=''> | <StructureSection load='5tnu' size='340' side='right'caption='[[5tnu]], [[Resolution|resolution]] 3.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5tnu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TNU OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5tnu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TNU FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 3.05Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5tnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tnu OCA], [https://pdbe.org/5tnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tnu RCSB], [https://www.ebi.ac.uk/pdbsum/5tnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tnu ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q970I2_SULTO Q970I2_SULTO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Much remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions. | |||
Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA.,Kahanda D, DuPrez KT, Hilario E, McWilliams MA, Wohlgamuth CH, Fan L, Slinker JD Anal Chem. 2018 Feb 6;90(3):2178-2185. doi: 10.1021/acs.analchem.7b04515. Epub, 2018 Jan 17. PMID:29285929<ref>PMID:29285929</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5tnu" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[ATPase 3D structures|ATPase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Sulfurisphaera tokodaii str. 7]] | ||
[[Category: | [[Category: DuPrez KT]] | ||
[[Category: | [[Category: Fan L]] | ||
[[Category: | [[Category: Hilario E]] | ||
[[Category: | [[Category: Wang I]] | ||
Latest revision as of 16:05, 4 October 2023
S. tokodaii XPB II crystal structure at 3.0 Angstrom resolutionS. tokodaii XPB II crystal structure at 3.0 Angstrom resolution
Structural highlights
FunctionPublication Abstract from PubMedMuch remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions. Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA.,Kahanda D, DuPrez KT, Hilario E, McWilliams MA, Wohlgamuth CH, Fan L, Slinker JD Anal Chem. 2018 Feb 6;90(3):2178-2185. doi: 10.1021/acs.analchem.7b04515. Epub, 2018 Jan 17. PMID:29285929[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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