1wcq: Difference between revisions
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==Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine.== | |||
<StructureSection load='1wcq' size='340' side='right'caption='[[1wcq]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1wcq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_viridifaciens Micromonospora viridifaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WCQ 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]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1wcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcq OCA], [https://pdbe.org/1wcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wcq RCSB], [https://www.ebi.ac.uk/pdbsum/1wcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NANH_MICVI NANH_MICVI] To release sialic acids for use as carbon and energy sources for this non-pathogenic bacterium while in pathogenic microorganisms, sialidases have been suggested to be pathogenic factors. | |||
== 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/wc/1wcq_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1wcq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Mutants of the Micromonospora viridifaciens sialidase, Y370E and Y370F, are catalytically active retaining enzymes that operate by different mechanisms. Previous substitutions with smaller amino acids, including Y370D, yielded inverting sialidases. At least one water molecule can fit into the active-site cavity of this mutant and act as a nucleophile from the face opposite the leaving group (Biochemistry 2003, 42, 12 682). Thus, addition of a CH(2) unit (Asp versus Glu) changes the mechanism from inversion back to retention of configuration. Based on Bronsted beta(lg) values, it is proposed that the Y370E mutant reacts by a double-displacement mechanism (beta(lg) on k(cat)/K(m) -0.36+/-0.04) with Glu370 acting as the nucleophile. However, the Y370F mutant (beta(lg) on k(cat)/K(m) -0.79+/-0.12) reacts via a dissociative transition state. The crystal structure of the Y370F mutant complexed with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid shows no significant active-site perturbation relative to the wild-type enzyme. | |||
Two nucleophilic mutants of the Micromonospora viridifaciens sialidase operate with retention of configuration by two different mechanisms.,Watson JN, Newstead S, Narine AA, Taylor G, Bennet AJ Chembiochem. 2005 Nov;6(11):1999-2004. PMID:16206228<ref>PMID:16206228</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1wcq" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Neuraminidase|Neuraminidase]] | *[[Neuraminidase 3D structures|Neuraminidase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Micromonospora viridifaciens]] | [[Category: Micromonospora viridifaciens]] | ||
[[Category: Bennet | [[Category: Bennet AJ]] | ||
[[Category: Newstead | [[Category: Newstead S]] | ||
[[Category: Taylor | [[Category: Taylor G]] | ||
[[Category: Watson | [[Category: Watson JN]] | ||
Latest revision as of 10:41, 23 October 2024
Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine.Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine.
Structural highlights
FunctionNANH_MICVI To release sialic acids for use as carbon and energy sources for this non-pathogenic bacterium while in pathogenic microorganisms, sialidases have been suggested to be pathogenic factors. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMutants of the Micromonospora viridifaciens sialidase, Y370E and Y370F, are catalytically active retaining enzymes that operate by different mechanisms. Previous substitutions with smaller amino acids, including Y370D, yielded inverting sialidases. At least one water molecule can fit into the active-site cavity of this mutant and act as a nucleophile from the face opposite the leaving group (Biochemistry 2003, 42, 12 682). Thus, addition of a CH(2) unit (Asp versus Glu) changes the mechanism from inversion back to retention of configuration. Based on Bronsted beta(lg) values, it is proposed that the Y370E mutant reacts by a double-displacement mechanism (beta(lg) on k(cat)/K(m) -0.36+/-0.04) with Glu370 acting as the nucleophile. However, the Y370F mutant (beta(lg) on k(cat)/K(m) -0.79+/-0.12) reacts via a dissociative transition state. The crystal structure of the Y370F mutant complexed with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid shows no significant active-site perturbation relative to the wild-type enzyme. Two nucleophilic mutants of the Micromonospora viridifaciens sialidase operate with retention of configuration by two different mechanisms.,Watson JN, Newstead S, Narine AA, Taylor G, Bennet AJ Chembiochem. 2005 Nov;6(11):1999-2004. PMID:16206228[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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