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| | <StructureSection load='5a6t' size='340' side='right'caption='[[5a6t]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='5a6t' size='340' side='right'caption='[[5a6t]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5a6t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii Sporosarcina pasteurii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5a6t]] 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=5A6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A6T FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.65Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </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=5a6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6t OCA], [https://pdbe.org/5a6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a6t RCSB], [https://www.ebi.ac.uk/pdbsum/5a6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6t 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=5a6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6t OCA], [http://pdbe.org/5a6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a6t RCSB], [http://www.ebi.ac.uk/pdbsum/5a6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6t ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/URE3_SPOPA URE3_SPOPA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Urease|Urease]] | + | *[[Urease 3D structures|Urease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Sporosarcina pasteurii]] | | [[Category: Sporosarcina pasteurii]] |
| - | [[Category: Urease]]
| + | [[Category: Benini S]] |
| - | [[Category: Benini, S]] | + | [[Category: Bertini L]] |
| - | [[Category: Bertini, L]] | + | [[Category: Cianci M]] |
| - | [[Category: Cianci, M]] | + | [[Category: Ciurli S]] |
| - | [[Category: Ciurli, S]] | + | [[Category: Mazzei L]] |
| - | [[Category: Mazzei, L]] | + | [[Category: Musiani F]] |
| - | [[Category: Musiani, F]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Sulfite]]
| + | |
| Structural highlights
5a6t is a 3 chain structure with sequence from Sporosarcina pasteurii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.65Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
URE3_SPOPA
Publication Abstract from PubMed
Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has also been suggested. In the present study, isothermal titration microcalorimetry was used to establish sulfite as a competitive inhibitor for S. pasteurii urease, with an inhibition constant of 0.19mM at pH7. The structure of the urease-sulfite complex, determined at 1.65A resolution, shows the inhibitor bound to the dinuclear Ni(II) center of urease in a tridentate mode involving bonds between the two Ni(II) ions in the active site and all three oxygen atoms of the inhibitor, supporting the observed competitive inhibition kinetics. This coordination mode of sulfite has never been observed, either in proteins or in small molecule complexes, and could inspire synthetic coordination chemists as well as biochemists to develop urease inhibitors based on this chemical moiety.
Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease.,Mazzei L, Cianci M, Benini S, Bertini L, Musiani F, Ciurli S J Inorg Biochem. 2015 Nov 5;154:42-49. doi: 10.1016/j.jinorgbio.2015.11.003. PMID:26580226[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Mazzei L, Cianci M, Benini S, Bertini L, Musiani F, Ciurli S. Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease. J Inorg Biochem. 2015 Nov 5;154:42-49. doi: 10.1016/j.jinorgbio.2015.11.003. PMID:26580226 doi:http://dx.doi.org/10.1016/j.jinorgbio.2015.11.003
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