2i42

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:05, 30 August 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2i42.gif|left|200px]]<br /><applet load="2i42" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2i42, resolution 2.2&Aring;" />
 
-
'''Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue'''<br />
 
-
==Overview==
+
==Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue==
-
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.
+
<StructureSection load='2i42' size='340' side='right'caption='[[2i42]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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='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='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='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>
 +
== 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.
 +
== 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/i4/2i42_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=2i42 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2I42 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica] with <scene name='pdbligand=I42:'>I42</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I42 OCA].
+
*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8637902 8637902]
+
[[Category: Large Structures]]
-
[[Category: Protein-tyrosine-phosphatase]]
+
-
[[Category: Single protein]]
+
[[Category: Yersinia enterocolitica]]
[[Category: Yersinia enterocolitica]]
-
[[Category: Saper, M A.]]
+
[[Category: Saper MA]]
-
[[Category: Vijayalakshmi, J.]]
+
[[Category: Vijayalakshmi J]]
-
[[Category: I42]]
+
-
[[Category: crystal structure]]
+
-
[[Category: transition state analogue]]
+
-
[[Category: vanadate]]
+
-
[[Category: yersinia ptpase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:48:50 2008''
+

Current revision

Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue

PDB ID 2i42

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/2i42"
Personal tools