7b58: Difference between revisions

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-'''Unreleased structure'''
-The entry 7b58 is ON HOLD  until Paper Publication
+==X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Cl determined at 1.72 Angstroms==
+<StructureSection load='7b58' size='340' side='right'caption='[[7b58]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7b58]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B58 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG:SILVER+ION'>AG</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7b58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b58 OCA], [https://pdbe.org/7b58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b58 RCSB], [https://www.ebi.ac.uk/pdbsum/7b58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b58 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/URE3_SPOPA URE3_SPOPA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Soft metal ions can inactivate urease, a Ni(II)-dependent enzyme whose hydrolytic activity has significant implications in agro-environmental science and human health. Kinetic and structural studies of the reaction of Canavalia ensiformis urease (JBU) and Sporosarcina pasteurii urease (SPU) with Ag(I) compounds of general formula [Ag(PEt(3))X](4) (X = Cl, Br, I), and with the ionic species [Ag(PEt(3))(2)]NO(3), revealed the role of the Ag(I) ion and its ligands in modulating the metal-enzyme interaction. The activity of JBU is obliterated by the [Ag(PEt(3))X](4) complexes, with IC(50) values in the nanomolar range; the efficiency of the inhibition increases in the Cl(-) &lt; Br(-) &lt; I(-) order. The activity of JBU upon [Ag(PEt(3))(2)]NO(3) addition decreases to a plateau corresponding to ca. 60% of the original activity and decreases with time at a reduced rate. Synchrotron X-ray crystallography on single crystals obtained after the incubation of SPU with the Ag(I) complexes yielded high-resolution (1.63-1.97 A) structures. The metal-protein adducts entail a dinuclear Ag(I) cluster bound to the conserved residues alphaCys322, alphaHis323, and alphaMet367, with a bridging cysteine thiolate atom, a weak Ag(...)Ag bond, and a quasi-linear Ag(I) coordination geometry. These observations suggest a mechanism that involves the initial substitution of the phosphine ligand, followed by a structural rearrangement to yield the dinuclear Ag(I) cluster. These findings indicate that urease, in addition to the active site dinuclear Ni(II) cluster, possesses a secondary metal binding site, located on the mobile flap domain, capable of recognizing pairs of soft metal ions and controlling catalysis.
-Authors: Mazzei, L., Cianci, M., Ciurli, S.
+Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes.,Mazzei L, Cirri D, Cianci M, Messori L, Ciurli S J Inorg Biochem. 2021 May;218:111375. doi: 10.1016/j.jinorgbio.2021.111375. Epub , 2021 Jan 29. PMID:33711632<ref>PMID:33711632</ref>
-Description: X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Cl determined at 1.72 Angstroms
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Cianci, M]]
+<div class="pdbe-citations 7b58" style="background-color:#fffaf0;"></div>
-[[Category: Mazzei, L]]
+== References ==
-[[Category: Ciurli, S]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Sporosarcina pasteurii]]
+[[Category: Cianci M]]
+[[Category: Ciurli S]]
+[[Category: Mazzei L]]