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2hrw

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(New page: 200px<br /><applet load="2hrw" size="350" color="white" frame="true" align="right" spinBox="true" caption="2hrw, resolution 2.200&Aring;" /> '''Crystal Structure o...)
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[[Image:2hrw.gif|left|200px]]<br /><applet load="2hrw" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2hrw, resolution 2.200&Aring;" />
 
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'''Crystal Structure of Phosphonopyruvate Hydrolase'''<br />
 
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==Overview==
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==Crystal Structure of Phosphonopyruvate Hydrolase==
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Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the, phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional, similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was, expressed in Escherichia coli and purified to homogeneity. Analytical gel, filtration indicated that the protein exists in solution predominantly as, a tetramer. The PPH pH rate profile indicates maximal activity over a, broad pH range. The steady-state kinetic constants determined for a rapid, equilibrium ordered kinetic mechanism with Mg2+ binding first (Kd = 140, +/- 40 microM), are kcat = 105 +/- 2 s(-1) and P-pyr Km = 5 +/- 1 microM., PEP (slow substrate kcat = 2 x 10(-4) s(-1)), oxalate, and sulfopyruvate, are competitive inhibitors with Ki values of 2.0 +/- 0.1 mM, 17 +/- 1, microM, and 210 +/- 10 microM, respectively. Three PPH crystal structures, have been determined, that of a ligand-free enzyme, the enzyme bound to, Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr, (substrate). The complex with the inhibitor was obtained by, cocrystallization, whereas that with the substrate was obtained by briefly, soaking crystals of the ligand-free enzyme with P-pyr prior to flash, cooling. The PPH structure resembles that of the other members of the, PEPM/ICL superfamily and is most similar to the functionally related, enzyme, PEPM. Each monomer of the dimer of dimers exhibits an, (alpha/beta)8 barrel fold with the eighth helix swapped between two, molecules of the dimer. Both P-pyr and oxalate are anchored to the active, site by Mg2+. The loop capping the active site is disordered in all three, structures, in contrast to PEPM, where the equivalent loop adopts an open, or disordered conformation in the unbound state but sequesters the, inhibitor from solvent in the bound state. Crystal packing may have, favored the open conformation of PPH even when the enzyme was, cocrystallized with the oxalate inhibitor. Structure alignment of PPH with, other superfamily members revealed two pairs of invariant or, conservatively replaced residues that anchor the flexible gating loop. The, proposed PPH catalytic mechanism is analogous to that of PEPM but includes, activation of a water nucleophile with the loop Thr118 residue.
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<StructureSection load='2hrw' size='340' side='right'caption='[[2hrw]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2hrw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Variovorax_sp._Pal2 Variovorax sp. Pal2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HRW FirstGlance]. <br>
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2HRW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Variovorax_sp._pal2 Variovorax sp. pal2] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HRW OCA].
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hrw OCA], [https://pdbe.org/2hrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hrw RCSB], [https://www.ebi.ac.uk/pdbsum/2hrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hrw ProSAT]</span></td></tr>
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Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily., Chen CC, Han Y, Niu W, Kulakova AN, Howard A, Quinn JP, Dunaway-Mariano D, Herzberg O, Biochemistry. 2006 Sep 26;45(38):11491-504. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16981709 16981709]
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</table>
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[[Category: Single protein]]
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== Function ==
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[[Category: Variovorax sp. pal2]]
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[https://www.uniprot.org/uniprot/PPHA_VARSP PPHA_VARSP] Hydrolyzes phosphonopyruvate. Not active towards phosphoenolpyruvate, glycerophosphate, phospho-L-serine or phosphoglycolic acid.<ref>PMID:12697754</ref>
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[[Category: Chen, C.C.H.]]
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== Evolutionary Conservation ==
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[[Category: Herzberg, O.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: CL]]
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Check<jmol>
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[[Category: NA]]
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<jmolCheckbox>
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[[Category: pep mutase/isocitrate lyase superfamily]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/2hrw_consurf.spt"</scriptWhenChecked>
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[[Category: phosphonopyruvate]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: phosphonopyruvate hydrolase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: phosphorus-carbon bond cleavage]]
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</jmolCheckbox>
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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=2hrw ConSurf].
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:27:18 2008''
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Variovorax sp. Pal2]]
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[[Category: Chen CCH]]
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[[Category: Herzberg O]]

Current revision

Crystal Structure of Phosphonopyruvate Hydrolase

PDB ID 2hrw

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