|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6qdy' size='340' side='right'caption='[[6qdy]], [[Resolution|resolution]] 1.42Å' scene=''> | | <StructureSection load='6qdy' size='340' side='right'caption='[[6qdy]], [[Resolution|resolution]] 1.42Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qdy]] 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=6QDY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QDY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qdy]] 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=6QDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QDY 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=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URE:UREA'>URE</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]] 1.416Å</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=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URE:UREA'>URE</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=6qdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qdy OCA], [https://pdbe.org/6qdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qdy RCSB], [https://www.ebi.ac.uk/pdbsum/6qdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qdy 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=6qdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qdy OCA], [http://pdbe.org/6qdy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qdy RCSB], [http://www.ebi.ac.uk/pdbsum/6qdy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qdy 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 == |
| Line 18: |
Line 19: |
| | </div> | | </div> |
| | <div class="pdbe-citations 6qdy" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6qdy" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Urease 3D structures|Urease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 24: |
Line 28: |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Sporosarcina pasteurii]] | | [[Category: Sporosarcina pasteurii]] |
| - | [[Category: Urease]]
| + | [[Category: Benini S]] |
| - | [[Category: Benini, S]] | + | [[Category: Cianci M]] |
| - | [[Category: Cianci, M]] | + | [[Category: Ciurli S]] |
| - | [[Category: Ciurli, S]] | + | [[Category: Mazzei L]] |
| - | [[Category: Mazzei, L]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Urea]]
| + | |
| Structural highlights
6qdy 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 1.416Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
URE3_SPOPA
Publication Abstract from PubMed
Urease, the most efficient enzyme known, contains an essential dinuclear Ni(II) cluster in the active site. It catalyzes the hydrolysis of urea, inducing a rapid pH increase that has negative effects on human health and agriculture. Thus, the control of urease activity is of utmost importance in medical, pharmaceutical, and agro-environmental applications. All known urease inhibitors are either toxic or inefficient. The development of new and efficient chemicals able to inhibit urease relies on the knowledge of all steps of the catalytic mechanism. The short (microseconds) lifetime of the urease-urea complex has hampered the determination of its structure. The present study uses fluoride to substitute the hydroxide acting as the co-substrate in the reaction, preventing the occurrence of the catalytic steps that follow substrate binding. The 1.42 A crystal structure of the urease-urea complex, reported here, resolves the enduring debate on the mechanism of this metalloenzyme.
The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme.,Mazzei L, Cianci M, Benini S, Ciurli S Angew Chem Int Ed Engl. 2019 May 27;58(22):7415-7419. doi:, 10.1002/anie.201903565. Epub 2019 Apr 30. PMID:30969470[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme. Angew Chem Int Ed Engl. 2019 May 27;58(22):7415-7419. doi:, 10.1002/anie.201903565. Epub 2019 Apr 30. PMID:30969470 doi:http://dx.doi.org/10.1002/anie.201903565
|
