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| | ==Crystal structure of the restriction endonuclease BstYI complex with DNA== | | ==Crystal structure of the restriction endonuclease BstYI complex with DNA== |
| - | <StructureSection load='1vrr' size='340' side='right' caption='[[1vrr]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='1vrr' size='340' side='right'caption='[[1vrr]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1vrr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yuv 1yuv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VRR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1vrr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yuv 1yuv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VRR FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sdo|1sdo]], [[1dfm|1dfm]], [[1bhm|1bhm]]</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]] 2.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bstYIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=1vrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vrr OCA], [https://pdbe.org/1vrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vrr RCSB], [https://www.ebi.ac.uk/pdbsum/1vrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vrr ProSAT]</span></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>
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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=1vrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vrr OCA], [http://pdbe.org/1vrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vrr RCSB], [http://www.ebi.ac.uk/pdbsum/1vrr PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q84AF2_GEOSE Q84AF2_GEOSE] |
| | <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: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Type II site-specific deoxyribonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Aggarwal, A K]] | + | [[Category: Aggarwal AK]] |
| - | [[Category: Samuelson, J C]] | + | [[Category: Samuelson JC]] |
| - | [[Category: Townson, S A]] | + | [[Category: Townson SA]] |
| - | [[Category: Xu, S Y]] | + | [[Category: Xu SY]] |
| - | [[Category: Double helix]]
| + | |
| - | [[Category: Enzyme-dna complex]]
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| - | [[Category: Hydrolase-dna complex]]
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| Structural highlights
Function
Q84AF2_GEOSE
Publication Abstract from PubMed
The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.,Townson SA, Samuelson JC, Xu SY, Aggarwal AK Structure. 2005 May;13(5):791-801. PMID:15893669[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Townson SA, Samuelson JC, Xu SY, Aggarwal AK. Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence. Structure. 2005 May;13(5):791-801. PMID:15893669 doi:S0969-2126(05)00130-9
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