1rql

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1rql" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rql, resolution 2.40&Aring;" /> '''Crystal Structure of...)
Current revision (08:24, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1rql.gif|left|200px]]<br /><applet load="1rql" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1rql, resolution 2.40&Aring;" />
 
-
'''Crystal Structure of Phosponoacetaldehyde Hydrolase Complexed with Magnesium and the Inhibitor Vinyl Sulfonate'''<br />
 
-
==Overview==
+
==Crystal Structure of Phosponoacetaldehyde Hydrolase Complexed with Magnesium and the Inhibitor Vinyl Sulfonate==
-
Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolytic, P-C bond cleavage of phosphonoacetaldehyde (Pald) to form orthophosphate, and acetaldehyde. The reaction proceeds via a Schiff-base intermediate, formed between Lys-53 and the Pald carbonyl. The x-ray crystal structures, of the wild-type phosphonatase complexed with Mg(II) alone or with Mg(II), plus vinylsulfonate (a phosphonoethylenamine analog) were determined to, 2.8 and 2.4 A, respectively. These structures were used to determine the, identity and positions of active site residues surrounding the Lys-53, ammonium group and the Pald carbonyl. These include Cys-22, His-56, Tyr-128, and Met-49. Site-directed mutagenesis was then employed to, determine whether or not these groups participate in catalysis. Based on, rate contributions, Tyr-128 and Cys-22 were eliminated as potential, catalytic groups. The Lys-53 epsilon-amino group, positioned for reaction, with the Pald carbonyl, forms a hydrogen bond with water 120. Water 120 is, also within hydrogen bond distance of an imidazole nitrogen of His-56 and, the sulfur atom of Met-49. Kinetic constants for mutants indicated that, His-56 (1000-fold reduction in k(cat)/K(m) upon Ala substitution) and, Met-49 (17,000-fold reduction in k(cat)/K(m) upon Leu substitution), function in catalysis of Schiff-base formation. Based on these results, it, is proposed that a network of hydrogen bonds among Lys-53, water 120, His-56, and Met-49 facilitate proton transfer from Lys-53 to the, carbinolamine intermediate. Comparison of the vinylsulfonate complex, versus unliganded structures indicated that association of the cap and, core domains is essential for the positioning of the Lys-53 for attack at, the Pald carbonyl and that substrate binding at the core domain stabilizes, cap domain binding.
+
<StructureSection load='1rql' size='340' side='right'caption='[[1rql]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1rql]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RQL FirstGlance]. <br>
-
1RQL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with MG and VSO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RQL OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VSO:VINYLSULPHONIC+ACID'>VSO</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rql OCA], [https://pdbe.org/1rql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rql RCSB], [https://www.ebi.ac.uk/pdbsum/1rql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rql ProSAT]</span></td></tr>
-
X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis., Morais MC, Zhang G, Zhang W, Olsen DB, Dunaway-Mariano D, Allen KN, J Biol Chem. 2004 Mar 5;279(10):9353-61. Epub 2003 Dec 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14670958 14670958]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PHNX_BACCE PHNX_BACCE] Involved in phosphonate degradation.
 +
== 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/rq/1rql_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=1rql ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus cereus]]
[[Category: Bacillus cereus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Allen, K.N.]]
+
[[Category: Allen KN]]
-
[[Category: Dunaway-Mariano, D.]]
+
[[Category: Dunaway-Mariano D]]
-
[[Category: Morais, M.C.]]
+
[[Category: Morais MC]]
-
[[Category: Olsen, D.B.]]
+
[[Category: Olsen DB]]
-
[[Category: Zhang, G.]]
+
[[Category: Zhang G]]
-
[[Category: Zhang, W.]]
+
[[Category: Zhang W]]
-
[[Category: MG]]
+
-
[[Category: VSO]]
+
-
[[Category: schiff-base formation; acid/base catalysis; structural enzymology; had superfamily]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:48:07 2007''
+

Current revision

Crystal Structure of Phosponoacetaldehyde Hydrolase Complexed with Magnesium and the Inhibitor Vinyl Sulfonate

PDB ID 1rql

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/1rql"
Personal tools