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5zmo

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Current revision (10:28, 27 March 2024) (edit) (undo)
 
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==Sulfur binding domain of ScoMcrA complexed with phosphorothioated DNA==
==Sulfur binding domain of ScoMcrA complexed with phosphorothioated DNA==
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<StructureSection load='5zmo' size='340' side='right' caption='[[5zmo]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
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<StructureSection load='5zmo' size='340' side='right'caption='[[5zmo]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5zmo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZMO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5zmo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)] and [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZMO FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCO4631 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmo OCA], [https://pdbe.org/5zmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zmo RCSB], [https://www.ebi.ac.uk/pdbsum/5zmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmo ProSAT]</span></td></tr>
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<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=5zmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zmo OCA], [http://pdbe.org/5zmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zmo RCSB], [http://www.ebi.ac.uk/pdbsum/5zmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zmo ProSAT]</span></td></tr>
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</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/Q9L0M9_STRCO Q9L0M9_STRCO]
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There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S(187)RGRR(191) loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.
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Structural basis for the recognition of sulfur in phosphorothioated DNA.,Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X, Zhao YL, Deng Z, Wu G, He X Nat Commun. 2018 Nov 8;9(1):4689. doi: 10.1038/s41467-018-07093-1. PMID:30409991<ref>PMID:30409991</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 5zmo" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Strco]]
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[[Category: Large Structures]]
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[[Category: Deng, Z]]
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[[Category: Streptomyces lividans]]
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[[Category: Fu, W]]
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[[Category: Deng Z]]
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[[Category: He, X]]
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[[Category: Fu W]]
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[[Category: He, Y]]
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[[Category: He X]]
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[[Category: Liu, G]]
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[[Category: He Y]]
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[[Category: Wu, G]]
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[[Category: Liu G]]
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[[Category: Yu, H]]
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[[Category: Wu G]]
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[[Category: Zhang, Z]]
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[[Category: Yu H]]
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[[Category: Zhao, Y]]
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[[Category: Zhang Z]]
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[[Category: Dna binding protein]]
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[[Category: Zhao Y]]
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[[Category: Dna binding protein-dna complex]]
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[[Category: Dna phosphorothioation]]
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[[Category: Type iv restriction endonuclease]]
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Current revision

Sulfur binding domain of ScoMcrA complexed with phosphorothioated DNA

PDB ID 5zmo

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