1a5o

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:27, 7 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1a5o.gif|left|200px]]<br /><applet load="1a5o" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1a5o, resolution 2.5&Aring;" />
 
-
'''K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL'''<br />
 
-
==Overview==
+
==K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL==
-
Klebsiella aerogenes urease possesses a dinuclear metallocenter in which, two nickel atoms are bridged by carbamylated Lys217. To assess whether, carbamate-specific chemistry is required for urease activity, site-directed mutagenesis and chemical rescue strategies were combined in, efforts to place a carboxylate group at the location of this metal ligand., Urease variants with Lys217 replaced by Glu, Cys, and Ala (K217E, K217C/C319A, and K217A proteins) were purified, shown to be activated by, incubation with small organic acids plus Ni(II), and structurally, characterized. K217C/C319A urease possessed a second change in which, Cys319 was replaced by Ala in order to facilitate efforts to chemically, modify Cys217; however, this covalent modification approach did not, produce active urease. Chemical rescue of the K217E, K217C/C319A, and, K217A variants required 2, 2, and 10 h, respectively, to reach maximal, activity levels. The highest activity generated [224 micromol of urea, degraded.min-1.(mg of protein)-1, for K217C/C319A urease incubated with, 500 mM formic acid and 10 mM Ni at pH 6.5] corresponded to 56% of that, measured for in vitro activation of the wild-type apoprotein. While the, K217E apoprotein showed minimal structural perturbations, the K217C/C319A, apoprotein showed a disordering of some active site residues, and the, K217A apoprotein revealed a repositioning of His219 to allow the formation, of a hydrogen bond with Thr169, thus replacing the hydrogen bond between, the amino group of Lys217 and Thr169 in the native enzyme. Importantly, these structures allow rationalization of the relative rates and yields of, chemical rescue experiments. The crystal structures of chemically rescued, K217A and K217C/C319A ureases revealed a return of the active site, residues to their wild-type positions. In both cases, noncovalently bound, formate was structurally equivalent to the Lys-carbamate as the bridging, metallocenter ligand. We conclude that carbamate-specific chemistry is not, required for urease catalysis.
+
<StructureSection load='1a5o' size='340' side='right'caption='[[1a5o]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1a5o]] 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=1A5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A5O 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]] 2.5&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1a5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a5o OCA], [https://pdbe.org/1a5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a5o RCSB], [https://www.ebi.ac.uk/pdbsum/1a5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a5o ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/URE3_KLEAE URE3_KLEAE]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/1a5o_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1a5o ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1A5O is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes] with NI and FMT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <scene name='pdbsite=ACT:Residue Implicated In Catalysis'>ACT</scene> and <scene name='pdbsite=NIL:Ni Metallocenter'>NIL</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1A5O OCA].
+
*[[Urease 3D structures|Urease 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand., Pearson MA, Schaller RA, Michel LO, Karplus PA, Hausinger RP, Biochemistry. 1998 Apr 28;37(17):6214-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9558361 9558361]
+
[[Category: Klebsiella aerogenes]]
[[Category: Klebsiella aerogenes]]
-
[[Category: Protein complex]]
+
[[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: Pearson MA]]
-
[[Category: Pearson, M.A.]]
+
[[Category: Schaller RA]]
-
[[Category: Schaller, R.A.]]
+
-
[[Category: FMT]]
+
-
[[Category: NI]]
+
-
[[Category: hydrolase (urea amido)]]
+
-
[[Category: mutant]]
+
-
[[Category: nickel metalloenzyme]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 14:09:23 2007''
+

Current revision

K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL

PDB ID 1a5o

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1a5o"
Personal tools