1rql: Difference between revisions

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<StructureSection load='1rql' size='340' side='right'caption='[[1rql]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1rql' size='340' side='right'caption='[[1rql]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rql]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. 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>
<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>
</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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fez|1fez]], [[1rqn|1rqn]]</div></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>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PHNX_BACCE PHNX_BACCE]] Involved in phosphonate degradation.  
[https://www.uniprot.org/uniprot/PHNX_BACCE PHNX_BACCE] Involved in phosphonate degradation.
== 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=1rql 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=1rql ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:14670958<ref>PMID:14670958</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rql" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 14579]]
[[Category: Bacillus cereus]]
[[Category: Large Structures]]
[[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: Acid/base catalysis]]
[[Category: Had superfamily]]
[[Category: Hydrolase]]
[[Category: Schiff-base formation]]
[[Category: Structural enzymology]]

Latest revision as of 11:24, 14 February 2024

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

Structural highlights

1rql is a 2 chain structure with sequence from Bacillus cereus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHNX_BACCE Involved in phosphonate degradation.

Evolutionary Conservation

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

1rql, resolution 2.40Å

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OCA
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