7cug: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolution== | ==Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolution== | ||
<StructureSection load='7cug' size='340' side='right'caption='[[7cug]]' scene=''> | <StructureSection load='7cug' size='340' side='right'caption='[[7cug]], [[Resolution|resolution]] 1.62Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CUG OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[7cug]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._TB-90 Bacillus sp. TB-90]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CUG FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.62Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=7cug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cug OCA], [https://pdbe.org/7cug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cug RCSB], [https://www.ebi.ac.uk/pdbsum/7cug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cug ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PUCL_BACSB PUCL_BACSB] Catalyzes two steps in the degradation of uric acid, i.e. the oxidation of uric acid to 5-hydroxyisourate (HIU) and the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Urate oxidases catalyze the cofactor-independent oxidation of uric acid, and an extensive water network in the active site has been suggested to play an essential role in the catalysis. For our present analysis of the structure and function of the water network, the crystal qualities of Bacillus sp. TB-90 urate oxidase (BTUO) were improved by controlled dehydration using the humid air and glue-coating method. After the dehydration, the P21212 crystals were transformed into the I222 space group, leading to an extension of the maximum resolution to 1.42 A. The dehydration of the crystals revealed a significant change in the five-water-molecules' binding mode in the vicinity of the catalytic diad, indicating that these molecules are quasi-stable. The pH profile analysis of log(kcat) gave two pKa values: pKa1 at 6.07 +/- 0.07 and pKa2 at 7.98 +/- 0.13. The site-directed mutagenesis of K13, T73, and N276 involved in the formation of the active-site water network revealed that the activities of these mutant variants were significantly reduced. These structural and kinetic data suggest that the five quasi-stable water molecules play an essential role in the catalysis of the cofactor-independent urate oxidation by reducing the energy penalty for the substrate-binding or an on-off switching for the proton-relay rectification. | |||
Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.,Hibi T, Itoh T J Biochem. 2020 Oct 1. pii: 5917020. doi: 10.1093/jb/mvaa114. PMID:33002140<ref>PMID:33002140</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7cug" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Urate oxidase 3D structures|Urate oxidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus sp. TB-90]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hibi T]] | [[Category: Hibi T]] | ||
[[Category: Itoh T]] | [[Category: Itoh T]] | ||
Latest revision as of 19:16, 29 November 2023
Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolutionCrystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.62 A resolution
Structural highlights
FunctionPUCL_BACSB Catalyzes two steps in the degradation of uric acid, i.e. the oxidation of uric acid to 5-hydroxyisourate (HIU) and the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (By similarity). Publication Abstract from PubMedUrate oxidases catalyze the cofactor-independent oxidation of uric acid, and an extensive water network in the active site has been suggested to play an essential role in the catalysis. For our present analysis of the structure and function of the water network, the crystal qualities of Bacillus sp. TB-90 urate oxidase (BTUO) were improved by controlled dehydration using the humid air and glue-coating method. After the dehydration, the P21212 crystals were transformed into the I222 space group, leading to an extension of the maximum resolution to 1.42 A. The dehydration of the crystals revealed a significant change in the five-water-molecules' binding mode in the vicinity of the catalytic diad, indicating that these molecules are quasi-stable. The pH profile analysis of log(kcat) gave two pKa values: pKa1 at 6.07 +/- 0.07 and pKa2 at 7.98 +/- 0.13. The site-directed mutagenesis of K13, T73, and N276 involved in the formation of the active-site water network revealed that the activities of these mutant variants were significantly reduced. These structural and kinetic data suggest that the five quasi-stable water molecules play an essential role in the catalysis of the cofactor-independent urate oxidation by reducing the energy penalty for the substrate-binding or an on-off switching for the proton-relay rectification. Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.,Hibi T, Itoh T J Biochem. 2020 Oct 1. pii: 5917020. doi: 10.1093/jb/mvaa114. PMID:33002140[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||