1ejt: Difference between revisions

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<StructureSection load='1ejt' size='340' side='right'caption='[[1ejt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1ejt' size='340' side='right'caption='[[1ejt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ejt]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJT FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ejt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJT FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ejr|1ejr]], [[1ejs|1ejs]], [[1eju|1eju]], [[1ejv|1ejv]], [[1ejw|1ejw]], [[1ejx|1ejx]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Urease Urease], with EC number [https://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=1ejt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejt OCA], [https://pdbe.org/1ejt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejt RCSB], [https://www.ebi.ac.uk/pdbsum/1ejt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejt 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=1ejt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejt OCA], [https://pdbe.org/1ejt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejt RCSB], [https://www.ebi.ac.uk/pdbsum/1ejt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/URE1_KLEAE URE1_KLEAE]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ejt ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ejt ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Klebsiella aerogenes urease uses a dinuclear nickel active site to catalyze urea hydrolysis at &gt;10(14)-fold the spontaneous rate. To better define the enzyme mechanism, we examined the kinetics and structures for a suite of site-directed variants involving four residues at the active site: His320, His219, Asp221, and Arg336. Compared to wild-type urease, the H320A, H320N, and H320Q variants exhibit similar approximately 10(-)(5)-fold deficiencies in rates, modest K(m) changes, and disorders in the peptide flap covering their active sites. The pH profiles for these mutant enzymes are anomalous with optima near 6 and shoulders that extend to pH 9. H219A urease exhibits 10(3)-fold increased K(m) over that of native enzyme, whereas the increase is less marked ( approximately 10(2)-fold) in the H219N and H219Q variants that retain hydrogen bonding capability. Structures for these variants show clearly resolved active site water molecules covered by well-ordered peptide flaps. Whereas the D221N variant is only moderately affected compared to wild-type enzyme, D221A urease possesses low activity ( approximately 10(-)(3) that of native enzyme), a small increase in K(m), and a pH 5 optimum. The crystal structure for D221A urease is reminiscent of the His320 variants. The R336Q enzyme has a approximately 10(-)(4)-fold decreased catalytic rate with near-normal pH dependence and an unaffected K(m). Phenylglyoxal inactivates the R336Q variant at over half the rate observed for native enzyme, demonstrating that modification of non-active-site arginines can eliminate activity, perhaps by affecting the peptide flap. Our data favor a mechanism in which His219 helps to polarize the substrate carbonyl group, a metal-bound terminal hydroxide or bridging oxo-dianion attacks urea to form a tetrahedral intermediate, and protonation occurs via the general acid His320 with Asp221 and Arg336 orienting and influencing the acidity of this residue. Furthermore, we conclude that the simple bell-shaped pH dependence of k(cat) and k(cat)/K(m) for the native enzyme masks a more complex underlying pH dependence involving at least four pK(a)s.
Kinetic and structural characterization of urease active site variants.,Pearson MA, Park IS, Schaller RA, Michel LO, Karplus PA, Hausinger RP Biochemistry. 2000 Jul 25;39(29):8575-84. PMID:10913264<ref>PMID:10913264</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ejt" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Urease 3D structures|Urease 3D structures]]
*[[Urease 3D structures|Urease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Klebsiella aerogenes]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Urease]]
[[Category: Hausinger RP]]
[[Category: Hausinger, R P]]
[[Category: Karplus PA]]
[[Category: Karplus, P A]]
[[Category: Michel LO]]
[[Category: Michel, L O]]
[[Category: Park IS]]
[[Category: Park, I S]]
[[Category: Pearson MA]]
[[Category: Pearson, M A]]
[[Category: Schaller RA]]
[[Category: Schaller, R A]]
[[Category: Alpha-beta barrel]]
[[Category: Hydrolase]]
[[Category: Nickel metalloenzyme]]

Latest revision as of 13:03, 20 March 2024

CRYSTAL STRUCTURE OF THE H219Q VARIANT OF KLEBSIELLA AEROGENES UREASECRYSTAL STRUCTURE OF THE H219Q VARIANT OF KLEBSIELLA AEROGENES UREASE

Structural highlights

1ejt is a 3 chain structure with sequence from Klebsiella aerogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

URE1_KLEAE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ejt, resolution 2.00Å

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