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| | ==Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA== | | ==Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA== |
| - | <StructureSection load='3v1z' size='340' side='right' caption='[[3v1z]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3v1z' size='340' side='right'caption='[[3v1z]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3v1z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V1Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3v1z]] 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=3V1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1Z FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3v20|3v20]], [[3v21|3v21]]</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bse634IR ([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=3v1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1z OCA], [https://pdbe.org/3v1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1z RCSB], [https://www.ebi.ac.uk/pdbsum/3v1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1z 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=3v1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1z OCA], [http://pdbe.org/3v1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v1z RCSB], [http://www.ebi.ac.uk/pdbsum/3v1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q8RT53_GEOSE Q8RT53_GEOSE] |
| - | Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the alpha6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.
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| - | Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.,Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V Nucleic Acids Res. 2012 Apr 11. PMID:22495930<ref>PMID:22495930</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 3v1z" 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: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Type II site-specific deoxyribonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Golovenko, D]] | + | [[Category: Golovenko D]] |
| - | [[Category: Grazulis, S]] | + | [[Category: Grazulis S]] |
| - | [[Category: Manakova, E N]] | + | [[Category: Manakova EN]] |
| - | [[Category: Tamulaitiene, G]] | + | [[Category: Tamulaitiene G]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Protein-dna complex]]
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| - | [[Category: Restriction endonuclease]]
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