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| | ==SgrAI with noncognate DNA bound== | | ==SgrAI with noncognate DNA bound== |
| - | <StructureSection load='3dpg' size='340' side='right' caption='[[3dpg]], [[Resolution|resolution]] 1.91Å' scene=''> | + | <StructureSection load='3dpg' size='340' side='right'caption='[[3dpg]], [[Resolution|resolution]] 1.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3dpg]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3dpg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.91Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sgraIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1911 Streptomyces griseus])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpg OCA], [https://pdbe.org/3dpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpg RCSB], [https://www.ebi.ac.uk/pdbsum/3dpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpg ProSAT]</span></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=3dpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpg RCSB], [http://www.ebi.ac.uk/pdbsum/3dpg PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q9F6L0_STRGR Q9F6L0_STRGR] |
| - | The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein-DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.
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| - | The structure of SgrAI bound to DNA; recognition of an 8 base pair target.,Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC Nucleic Acids Res. 2008 Sep;36(16):5405-16. Epub 2008 Aug 13. PMID:18701646<ref>PMID:18701646</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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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Streptomyces griseus]] | | [[Category: Streptomyces griseus]] |
| - | [[Category: Type II site-specific deoxyribonuclease]]
| + | [[Category: Dunten PW]] |
| - | [[Category: Dunten, P W]] | + | [[Category: Horton NC]] |
| - | [[Category: Horton, N C]] | + | [[Category: Little EJ]] |
| - | [[Category: Little, E J]] | + | |
| - | [[Category: Base-pair mismatch]]
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| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Restriction enzyme-dna complex]]
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