1xg3

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[[Image:1xg3.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate==
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|PDB= 1xg3 |SIZE=350|CAPTION= <scene name='initialview01'>1xg3</scene>, resolution 1.9&Aring;
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<StructureSection load='1xg3' size='340' side='right'caption='[[1xg3]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>
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<table><tr><td colspan='2'>[[1xg3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XG3 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylisocitrate_lyase Methylisocitrate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.30 4.1.3.30] </span>
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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]] 1.9&#8491;</td></tr>
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|GENE= prpB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=1xg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xg3 OCA], [https://pdbe.org/1xg3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xg3 RCSB], [https://www.ebi.ac.uk/pdbsum/1xg3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xg3 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1oqf|1oqf]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xg3 OCA], [http://www.ebi.ac.uk/pdbsum/1xg3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xg3 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PRPB_ECOLI PRPB_ECOLI] Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate.<ref>PMID:11422389</ref> <ref>PMID:15723538</ref>
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== Evolutionary Conservation ==
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'''Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate'''
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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/xg/1xg3_consurf.spt"</scriptWhenChecked>
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Two crystal structures of the C123S mutant of 2-methylisocitrate lyase have been determined, one with the bound reaction products, Mg(2+)-pyruvate and succinate, and the second with a bound Mg(2+)-(2R,3S)-isocitrate inhibitor. Comparison with the structure of the wild-type enzyme in the unbound state reveals that the enzyme undergoes a conformational transition that sequesters the ligand from solvent, as previously observed for two other enzyme superfamily members, isocitrate lyase and phosphoenolpyruvate mutase. The binding modes reveal the determinants of substrate specificity and stereoselectivity, and the stringent specificity is verified in solution using various potential substrates. A model of bound 2-methylisocitrate has been developed based on the experimentally determined structures. We propose a catalytic mechanism involving an alpha-carboxy-carbanion intermediate/transition state, which is consistent with previous stereochemical experiments showing inversion of configuration at the C(3) of 2-methylisocitrate. Structure-based sequence analysis and phylogenic tree construction reveal determinants of substrate specificity, highlight nodes of divergence of families, and predict enzyme families with new functions.
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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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1XG3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XG3 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=1xg3 ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution., Liu S, Lu Z, Han Y, Melamud E, Dunaway-Mariano D, Herzberg O, Biochemistry. 2005 Mar 1;44(8):2949-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15723538 15723538]
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Methylisocitrate lyase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Dunaway-Mariano D]]
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[[Category: Dunaway-Mariano, D.]]
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[[Category: Han Y]]
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[[Category: Han, Y.]]
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[[Category: Herzberg O]]
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[[Category: Herzberg, O.]]
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[[Category: Liu S]]
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[[Category: Liu, S.]]
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[[Category: Lu Z]]
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[[Category: Lu, Z.]]
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[[Category: Melamud E]]
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[[Category: Melamud, E.]]
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[[Category: 2-methylisocitrate lyase/product complex]]
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[[Category: isocitrate lyase superfamily]]
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[[Category: pyruvate]]
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[[Category: succinate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:49:08 2008''
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Current revision

Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate

PDB ID 1xg3

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