2i42: Difference between revisions

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<StructureSection load='2i42' size='340' side='right'caption='[[2i42]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2i42' size='340' side='right'caption='[[2i42]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2i42]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_enterocoliticum"_schleifstein_and_coleman_1939 "bacterium enterocoliticum" schleifstein and coleman 1939]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I42 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2i42]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I42 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</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]] 2.2&#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;'>[[1yts|1yts]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 "Bacterium enterocoliticum" Schleifstein and Coleman 1939])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=2i42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i42 OCA], [https://pdbe.org/2i42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i42 RCSB], [https://www.ebi.ac.uk/pdbsum/2i42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i42 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=2i42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i42 OCA], [https://pdbe.org/2i42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i42 RCSB], [https://www.ebi.ac.uk/pdbsum/2i42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i42 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN]] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.  
[https://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i4/2i42_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i4/2i42_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
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<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Engineering site-specific amino acid substitutions into the protein-tyrosine phosphatase (PTPase) PTP1 and the dual-specific vaccinia H1-related phosphatase (VHR), has kinetically isolated the two chemical steps of the reaction and provided a rare opportunity for examining transition states and directly observing the phosphoenzyme intermediate. Changing serine to alanine in the active-site sequence motif HCXXGXXRS shifted the rate-limiting step from intermediate formation to intermediate hydrolysis. Using phosphorus 31P NMR, the covalent thiol-phosphate intermediate was directly observed during catalytic turnover. The importance of the conserved aspartic acid (D92 in VHR and D181 in PTP1) in both chemical steps was established. Kinetic analysis of D92N and D181N mutants indicated that aspartic acid acts as a general acid by protonating the leaving-group phenolic oxygen. Structure-reactivity experiments with native and aspartate mutant enzymes established that proton transfer is concomitant with P-O cleavage, such that no charge develops on the phenolic oxygen. Steady- and presteady-state kinetics, as well as NMR analysis of the double mutant D92N/S131A (VHR), suggested that the conserved aspartic acid functions as a general base during intermediate hydrolysis. As a general base, aspartate would activate a water molecule to facilitate nucleophilic attack. The amino acids involved in transition-state stabilization for cysteinylphosphate hydrolysis were confirmed by the x-ray structure of the Yersinia PTPase complexed with vanadate, a transition-state mimic that binds covalently to the active-site cysteine. Consistent with the NMR, x-ray, biochemical, and kinetic data, a unifying mechanism for catalysis is proposed.
Protein-tyrosine phosphatases (PTPases) contain an evolutionarily conserved segment of 250 amino acids referred to as the PTPase catalytic domain. The recombinant PTPase domain from Yersinia enterocolitica enhances the rate of hydrolysis of p-nitrophenyl phosphate, a phosphate monoester, by approximately 10(11) over the non-enzyme-catalyzed rate by water. Specific amino acid residues responsible for the catalytic rate acceleration have been examined by site-directed mutagenesis. Our results suggest that Asp-356 (D356) and Glu-290 (E290) are the general acid and the general base catalysts responsible for Yersinia PTPase-catalyzed phosphate ester hydrolysis. The PTPase with both E290Q and D356N mutations shows no pH dependence for catalysis but displays a rate enhancement of 2.6 x 10(6), compared to the noncatalyzed hydrolysis of p-nitrophenyl phosphate by water. This rate enhancement probably occurs via transition-state stabilization. Our results suggest that all PTP-ases use a common mechanism that depends upon formation of a thiol-phosphate intermediate and general acid-general base catalysis.


Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis.,Denu JM, Lohse DL, Vijayalakshmi J, Saper MA, Dixon JE Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2493-8. PMID:8637902<ref>PMID:8637902</ref>
Dissecting the catalytic mechanism of protein-tyrosine phosphatases.,Zhang ZY, Wang Y, Dixon JE Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1624-7. PMID:008127855<ref>PMID:008127855</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacterium enterocoliticum schleifstein and coleman 1939]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Protein-tyrosine-phosphatase]]
[[Category: Yersinia enterocolitica]]
[[Category: Saper, M A]]
[[Category: Saper MA]]
[[Category: Vijayalakshmi, J]]
[[Category: Vijayalakshmi J]]
[[Category: Hydrolase]]
[[Category: Transition state analogue]]
[[Category: Vanadate]]
[[Category: Yersinia ptpase]]
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