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| | <StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DC1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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]] 1.7Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://pdbe.org/1dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 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=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE]] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1. | + | [https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
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| - | BACKGROUND: Restriction endonucleases form a diverse family of proteins with substantial variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a thermophilic restriction endonuclease that exhibits both base-specific and degenerate recognition within the sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate DNA has been determined to 1.7 A resolution, revealing several unprecedented features. Each BsoBI monomer is formed by inserting a helical domain into an expanded EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition sequence DNA lies within a 20 A long tunnel of protein that excludes bulk solvent. Interactions with the specific bases are made in both grooves through direct and water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is positioned to act as a general base. CONCLUSIONS: A catalytic mechanism employing His253 and two metal ions is proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a restriction endonuclease. The structure also provides two novel examples of the role of water in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by the absence of bulk solvent.
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| - | Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.,van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM Structure. 2001 Feb 7;9(2):133-44. PMID:11250198<ref>PMID:11250198</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 1dc1" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Endonuclease|Endonuclease]] | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Geobacillus stearothermophilus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Type II site-specific deoxyribonuclease]]
| + | [[Category: Friedman AM]] |
| - | [[Category: Friedman, A M]] | + | [[Category: Pelletier JJ]] |
| - | [[Category: Pelletier, J J]] | + | [[Category: Xu S-Y]] |
| - | [[Category: Woerd, M J.van der]]
| + | [[Category: Van der Woerd MJ]] |
| - | [[Category: Xu, S Y]] | + | |
| - | [[Category: Degenerate dna recognition]] | + | |
| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Protein-dna complex]]
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| - | [[Category: Restriction endonuclease]]
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| - | [[Category: Thermophilic enzyme]]
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