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| | <StructureSection load='7ccd' size='340' side='right'caption='[[7ccd]], [[Resolution|resolution]] 2.42Å' scene=''> | | <StructureSection load='7ccd' size='340' side='right'caption='[[7ccd]], [[Resolution|resolution]] 2.42Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7ccd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_pristinaespiralis"_mancy_et_al. "streptomyces pristinaespiralis" mancy et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CCD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CCD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7ccd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B7A Escherichia coli B7A] and [https://en.wikipedia.org/wiki/Streptomyces_pristinaespiralis Streptomyces pristinaespiralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CCD FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</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]] 2.42Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7cc9|7cc9]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SPRI_5136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38300 "Streptomyces pristinaespiralis" Mancy et al.])</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=7ccd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ccd OCA], [https://pdbe.org/7ccd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ccd RCSB], [https://www.ebi.ac.uk/pdbsum/7ccd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ccd ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7ccd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ccd OCA], [http://pdbe.org/7ccd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7ccd RCSB], [http://www.ebi.ac.uk/pdbsum/7ccd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7ccd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0M4DML1_STRPR A0A0M4DML1_STRPR] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Streptomyces pristinaespiralis mancy et al]] | + | [[Category: Escherichia coli B7A]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Deng, Z]] | + | [[Category: Streptomyces pristinaespiralis]] |
| - | [[Category: Gan, J]] | + | [[Category: Deng Z]] |
| - | [[Category: He, X]] | + | [[Category: Gan J]] |
| - | [[Category: Hu, W]] | + | [[Category: He X]] |
| - | [[Category: Li, J]] | + | [[Category: Hu W]] |
| - | [[Category: Liu, G]] | + | [[Category: Li J]] |
| - | [[Category: Wang, Y]] | + | [[Category: Liu G]] |
| - | [[Category: Yu, H]] | + | [[Category: Wang Y]] |
| - | [[Category: Zhao, G]] | + | [[Category: Yu H]] |
| - | [[Category: Zhao, Y]] | + | [[Category: Zhao G]] |
| - | [[Category: Dna binding protein]]
| + | [[Category: Zhao Y]] |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Phosphorothioated dna]]
| + | |
| - | [[Category: Restriction enzyme]]
| + | |
| - | [[Category: Sulfur binding domain]]
| + | |
| Structural highlights
Function
A0A0M4DML1_STRPR
Publication Abstract from PubMed
The sulfur atom of phosphorothioated DNA (PT-DNA) is coordinated by a surface cavity in the conserved sulfur-binding domain (SBD) of type IV restriction enzymes. However, some SBDs cannot recognize the sulfur atom in some sequence contexts. To illustrate the structural determinants for sequence specificity, we resolved the structure of SBDSpr, from endonuclease SprMcrA, in complex with DNA of GPSGCC, GPSATC and GPSAAC contexts. Structural and computational analyses explained why it binds the above PT-DNAs with an affinity in a decreasing order. The structural analysis of SBDSpr-GPSGCC and SBDSco-GPSGCC, the latter only recognizes DNA of GPSGCC, revealed that a positively charged loop above the sulfur-coordination cavity electrostatically interacts with the neighboring DNA phosphate linkage. The structural analysis indicated that the DNA-protein hydrogen bonding pattern and weak non-bonded interaction played important roles in sequence specificity of SBD protein. Exchanges of the positively-charged amino acid residues with the negatively-charged residues in the loop would enable SBDSco to extend recognization for more PT-DNA sequences, implying that type IV endonucleases can be engineered to recognize PT-DNA in novel target sequences.
DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.,Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X Nucleic Acids Res. 2020 Sep 4;48(15):8755-8766. doi: 10.1093/nar/gkaa574. PMID:32621606[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X. DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses. Nucleic Acids Res. 2020 Sep 4;48(15):8755-8766. doi: 10.1093/nar/gkaa574. PMID:32621606 doi:http://dx.doi.org/10.1093/nar/gkaa574
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