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| | ==Crystal structure of DndA from streptomyces lividans== | | ==Crystal structure of DndA from streptomyces lividans== |
| - | <StructureSection load='3vax' size='340' side='right' caption='[[3vax]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3vax' size='340' side='right'caption='[[3vax]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vax]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VAX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vax]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VAX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.4Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dndA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vax OCA], [http://pdbe.org/3vax PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vax RCSB], [http://www.ebi.ac.uk/pdbsum/3vax PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vax 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=3vax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vax OCA], [https://pdbe.org/3vax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vax RCSB], [https://www.ebi.ac.uk/pdbsum/3vax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vax ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A7TUX7_STRLI A7TUX7_STRLI] |
| - | DNA phosphorothioation is widespread among prokaryotes, and might function to restrict gene transfer among different kinds of bacteria. There has been little investigation into the structural mechanism of the DNA phosphorothioation process. DndA is a cysteine desulfurase which is involved in the first step of DNA phosphorothioation. In this study, we determined the crystal structure of Streptomyces lividans DndA in complex with its covalently bound cofactor PLP, to a resolution of 2.4 A. Our structure reveals the molecular mechanism that DndA employs to recognize its cofactor PLP, and suggests the potential binding site for the substrate L-cysteine on DndA. In contrast to previously determined structures of cysteine desulfurases, the catalytic cysteine of DndA was found to reside on a beta strand. This catalytic cysteine is very far away from the presumable location of the substrate, suggesting that a conformational change of DndA is required during the catalysis process to bring the catalytic cysteine close to the substrate cysteine. Moreover, our in vitro enzymatic assay results suggested that this conformational change is unlikely to be a simple result of random thermal motion, since moving the catalytic cysteine two residues forward or backward in the primary sequence completely disabled the cysteine desulfurase activity of DndA.
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| - | Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation.,Chen F, Zhang Z, Lin K, Qian T, Zhang Y, You D, He X, Wang Z, Liang J, Deng Z, Wu G PLoS One. 2012;7(5):e36635. doi: 10.1371/journal.pone.0036635. Epub 2012 May 3. PMID:22570733<ref>PMID:22570733</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3vax" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces lividans krasil'nikov et al. 1965]] | + | [[Category: Large Structures]] |
| - | [[Category: Chen, F]] | + | [[Category: Streptomyces lividans]] |
| - | [[Category: Lin, K]] | + | [[Category: Chen F]] |
| - | [[Category: Wu, G]] | + | [[Category: Lin K]] |
| - | [[Category: Zhang, Z]] | + | [[Category: Wu G]] |
| - | [[Category: Desulfurase]]
| + | [[Category: Zhang Z]] |
| - | [[Category: Transferase]]
| + | |
