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2dua

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[[Image:2dua.jpg|left|200px]]
 
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{{Structure
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==Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++==
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|PDB= 2dua |SIZE=350|CAPTION= <scene name='initialview01'>2dua</scene>, resolution 2.000&Aring;
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<StructureSection load='2dua' size='340' side='right'caption='[[2dua]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>
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<table><tr><td colspan='2'>[[2dua]] 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=2DUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUA FirstGlance]. <br>
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|ACTIVITY=
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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&#8491;</td></tr>
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|GENE= pphA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=218557 Variovorax sp. Pal2])
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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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
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|DOMAIN=
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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=2dua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dua OCA], [https://pdbe.org/2dua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dua RCSB], [https://www.ebi.ac.uk/pdbsum/2dua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dua ProSAT]</span></td></tr>
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|RELATEDENTRY=[[2hjp|2HJP]], [[2hrw|2HRW]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dua OCA], [http://www.ebi.ac.uk/pdbsum/2dua PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dua RCSB]</span>
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== Function ==
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}}
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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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== Evolutionary Conservation ==
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'''Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dua_consurf.spt"</scriptWhenChecked>
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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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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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2DUA is a [[Single protein]] structure of sequence from [http://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=2DUA OCA].
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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=2dua ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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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://www.ncbi.nlm.nih.gov/pubmed/16981709 16981709]
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<references/>
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[[Category: Single protein]]
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__TOC__
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[[Category: Variovorax sp. pal2]]
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</StructureSection>
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[[Category: Chen, C.]]
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[[Category: Large Structures]]
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[[Category: Herzberg, O.]]
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[[Category: Variovorax sp. Pal2]]
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[[Category: pep mutase/isocitrate lyase superfamily]]
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[[Category: Chen C]]
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[[Category: phosphonopyruvate]]
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[[Category: Herzberg O]]
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[[Category: phosphonopyruvate hydrolase]]
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[[Category: phosphorus-carbon bond cleavage]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:39:35 2008''
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Current revision

Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++

PDB ID 2dua

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