3n7b: Difference between revisions

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<StructureSection load='3n7b' size='340' side='right'caption='[[3n7b]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
<StructureSection load='3n7b' size='340' side='right'caption='[[3n7b]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3n7b]] 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=3N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N7B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3n7b]] 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=3N7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N7B FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dw9|3dw9]], [[3dvo|3dvo]], [[3dpg|3dpg]], [[3mqy|3mqy]], [[3n78|3n78]]</div></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='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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n7b OCA], [https://pdbe.org/3n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n7b RCSB], [https://www.ebi.ac.uk/pdbsum/3n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n7b 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=3n7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n7b OCA], [https://pdbe.org/3n7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n7b RCSB], [https://www.ebi.ac.uk/pdbsum/3n7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n7b 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]
SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-activation with expansion of DNA-sequence specificity. The three-dimensional crystal structures of SgrAI bound to cleaved primary-site DNA and Mg(2)(+) and bound to secondary-site DNA with either Mg(2)(+) or Ca(2)(+) are presented. All three structures show a conformation of enzyme and DNA similar to the previously determined dimeric structure of SgrAI bound to uncleaved primary-site DNA and Ca(2)(+) [Dunten et al. (2008), Nucleic Acids Res. 36, 5405-5416], with the exception of the cleaved bond and a slight shifting of the DNA in the SgrAI/cleaved primary-site DNA/Mg(2)(+) structure. In addition, a new metal ion binding site is located in one of the two active sites in this structure, which is consistent with proposals for the existence of a metal-ion site near the 3'-O leaving group.
 
New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA.,Little EJ, Dunten PW, Bitinaite J, Horton NC Acta Crystallogr D Biol Crystallogr. 2011 Jan;67(Pt 1):67-74. Epub 2010, Dec 16. PMID:21206063<ref>PMID:21206063</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3n7b" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__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]]
[[Category: Restriction endonuclease]]

Latest revision as of 09:59, 14 February 2024

SgrAI bound to secondary site DNA and Ca(II)

3n7b, resolution 2.65Å

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