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7x4e

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<StructureSection load='7x4e' size='340' side='right'caption='[[7x4e]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
<StructureSection load='7x4e' size='340' side='right'caption='[[7x4e]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7x4e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7X4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7X4E FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7x4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronorubrum_bangense_JCM_10635 Natronorubrum bangense JCM 10635]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7X4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7X4E FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7x4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7x4e OCA], [https://pdbe.org/7x4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7x4e RCSB], [https://www.ebi.ac.uk/pdbsum/7x4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7x4e 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=7x4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7x4e OCA], [https://pdbe.org/7x4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7x4e RCSB], [https://www.ebi.ac.uk/pdbsum/7x4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7x4e ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[[https://www.uniprot.org/uniprot/L9WJT3_9EURY L9WJT3_9EURY]]
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Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 A. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification. IMPORTANCE DndABCDE proteins have been demonstrated to catalyze DNA PT modification with the nonbridging oxygen in the DNA sugar-phosphate backbone replaced by sulfur. In the PT modification pathway, DndA exerts cysteine desulfurase activity capable of catalyzing the mobilization of sulfur from l-cysteine, which involves the ion-sulfur cluster assembly of DndC. This is regarded as the initial step of the DNA PT modification. Moreover, DndD has ATPase activity in vitro, which is believed to provide energy for the oxygen-sulfur swap, while the function of DndE is unknown. However, the exact function of the key enzyme DndE remains to be elucidated. By determining the structure of DndE from the haloalkaliphilic strain Natronorubrum bangense JCM10635, we showed that the archaeal DndE adopts a monomer conformation. Notably, DndE can introduce nicks to supercoiled DNA and exhibits a binding preference for nicked DNA; the nicking is believed to be the initial step for DNA to facilitate the sulfur incorporation.
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Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.,He W, Gao H, Wu D, Jiang S, Huang W, Chen C, Deng Z, Xiong L, Wu G, Wang L mBio. 2022 Apr 14:e0071622. doi: 10.1128/mbio.00716-22. PMID:35420474<ref>PMID:35420474</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7x4e" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Chen, S]]
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[[Category: Natronorubrum bangense JCM 10635]]
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[[Category: Haiyan, G]]
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[[Category: Chen S]]
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[[Category: Wang, L]]
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[[Category: Haiyan G]]
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[[Category: Wei, H]]
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[[Category: Wang L]]
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[[Category: Wu, G]]
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[[Category: Wei H]]
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[[Category: Dna binding protein]]
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[[Category: Wu G]]
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[[Category: Dnase]]
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Revision as of 06:28, 8 September 2022

Structure of 10635-DndE

PDB ID 7x4e

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