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| | <StructureSection load='3dw9' size='340' side='right'caption='[[3dw9]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='3dw9' size='340' side='right'caption='[[3dw9]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3dw9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_griseus"_krainsky_1914 "actinomyces griseus" krainsky 1914]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DW9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3dw9]] 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=3DW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DW9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dpg|3dpg]], [[3dvo|3dvo]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sgraIR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1911 "Actinomyces griseus" Krainsky 1914])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dw9 OCA], [https://pdbe.org/3dw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dw9 RCSB], [https://www.ebi.ac.uk/pdbsum/3dw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dw9 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=3dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dw9 OCA], [https://pdbe.org/3dw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dw9 RCSB], [https://www.ebi.ac.uk/pdbsum/3dw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dw9 ProSAT]</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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| - | <div class="pdbe-citations 3dw9" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces griseus krainsky 1914]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Type II site-specific deoxyribonuclease]] | + | [[Category: Streptomyces griseus]] |
| - | [[Category: Dunten, P W]] | + | [[Category: Dunten PW]] |
| - | [[Category: Horton, N C]] | + | [[Category: Horton NC]] |
| - | [[Category: Little, E J]] | + | [[Category: Little EJ]] |
| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Restriction enzyme-dna complex]]
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