1k0z

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<StructureSection load='1k0z' size='340' side='right'caption='[[1k0z]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
<StructureSection load='1k0z' size='340' side='right'caption='[[1k0z]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1k0z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0Z FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1k0z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0Z FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pvu|1pvu]], [[1pvi|1pvi]], [[1foo|1foo]], [[2pvi|2pvi]], [[3pvi|3pvi]], [[1eyu|1eyu]]</div></td></tr>
 
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PvuiiR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</td></tr>
 
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<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=1k0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0z OCA], [https://pdbe.org/1k0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0z RCSB], [https://www.ebi.ac.uk/pdbsum/1k0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0z 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=1k0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0z OCA], [https://pdbe.org/1k0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0z RCSB], [https://www.ebi.ac.uk/pdbsum/1k0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0z ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/T2P2_PROHU T2P2_PROHU]] Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.
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[https://www.uniprot.org/uniprot/T2P2_PROHU T2P2_PROHU] Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The rational design and X-ray crystallographic analyses of two symmetrical allosteric effectors of hemoglobin (Hb) are reported. Compound design was directed by the previously solved co-crystal structure of one of the most potent allosteric effectors of Hb, 2-[4-[(3,5-dichlorophenylcarbamoyl)-methyl]-phenoxy]-2-methylpropionic acid (RSR4), which revealed two distinct binding sites for this compound in the Hb central water cavity. The primary binding site has been observed for all compounds of this structural class, which stabilize deoxy Hb by engaging in inter-dimer contacts with three of the four protein subunits. Interactions at the secondary binding site of RSR4 occur primarily between the beta(1) and beta(2) subunits and serve to further constrain the deoxy state. Based on these observations, it was hypothesized that compounds with the ability to simultaneously span and link both of these sites would possess increased potency, but at a lower molar concentration than RSR4. Two symmetrical compounds were designed and synthesized based on this hypothesis. The symmetrical effector approach was taken to minimize the number of compound orientations needed to successfully bind at either of the distinct allosteric sites. X-ray crystallographic analyses of these two effectors in complex with Hb revealed that they successfully spanned the RSR4 primary and secondary binding sites. However, the designed compounds interacted with the secondary binding site in such a way that intra-dimer, as opposed to inter-dimer, interactions were generated. In agreement with these observations, in vitro evaluation of the symmetrical effectors in Hb solution indicated that neither compound possessed the potency of RSR4. A detailed analysis of symmetrical effector-Hb contacts and comparisons with the binding contacts of RSR4 are discussed.
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X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites.,Safo MK, Boyiri T, Burnett JC, Danso-Danquah R, Moure CM, Joshi GS, Abraham DJ Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):634-44. Epub 2002, Mar 22. PMID:11914488<ref>PMID:11914488</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1k0z" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 29905]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Proteus vulgaris]]
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[[Category: Athanasiadis, A]]
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[[Category: Athanasiadis A]]
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[[Category: Jeltsch, A]]
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[[Category: Jeltsch A]]
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[[Category: Kokkinidis, M]]
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[[Category: Kokkinidis M]]
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[[Category: Lanio, T]]
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[[Category: Lanio T]]
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[[Category: Matzen, C]]
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[[Category: Matzen C]]
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[[Category: Pingoud, A]]
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[[Category: Pingoud A]]
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[[Category: Scheuring-Vanamee, E]]
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[[Category: Scheuring-Vanamee E]]
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[[Category: Simoncsits, A]]
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[[Category: Simoncsits A]]
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[[Category: Spyridaki, A]]
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[[Category: Spyridaki A]]
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[[Category: Catalysis]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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[[Category: Ion]]
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[[Category: Lanthanade]]
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[[Category: Pvuii]]
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[[Category: Restriction enzyme]]
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[[Category: Xray]]
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Revision as of 12:22, 1 February 2023

Crystal Structure of the PvuII endonuclease with Pr3+ and SO4 ions bound in the active site at 2.05A.

PDB ID 1k0z

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