1oqf

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(New page: 200px<br /><applet load="1oqf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1oqf, resolution 1.93&Aring;" /> '''Crystal structure of...)
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[[Image:1oqf.gif|left|200px]]<br /><applet load="1oqf" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1oqf, resolution 1.93&Aring;" />
 
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'''Crystal structure of the 2-methylisocitrate lyase'''<br />
 
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==Overview==
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==Crystal structure of the 2-methylisocitrate lyase==
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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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<StructureSection load='1oqf' size='340' side='right'caption='[[1oqf]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1oqf]] is a 2 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=1OQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQF FirstGlance]. <br>
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1OQF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OQF 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]] 1.93&#8491;</td></tr>
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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=1oqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqf OCA], [https://pdbe.org/1oqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqf RCSB], [https://www.ebi.ac.uk/pdbsum/1oqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqf ProSAT]</span></td></tr>
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==Reference==
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</table>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15723538 15723538]
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== Function ==
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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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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/1oqf_consurf.spt"</scriptWhenChecked>
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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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</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=1oqf ConSurf].
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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>
[[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: 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: S2F, Structure.2.Function.Project.]]
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[[Category: alpha-beta barrel]]
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[[Category: s2f]]
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[[Category: structural genomics]]
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[[Category: structure 2 function project]]
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[[Category: swapped helix across a dimer]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:06:18 2007''
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Current revision

Crystal structure of the 2-methylisocitrate lyase

PDB ID 1oqf

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