2i6k

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[[Image:2i6k.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of human type I IPP isomerase complexed with a substrate analog==
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|PDB= 2i6k |SIZE=350|CAPTION= <scene name='initialview01'>2i6k</scene>, resolution 2.00&Aring;
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<StructureSection load='2i6k' size='340' side='right'caption='[[2i6k]], [[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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=EA2:AMINOETHANOLPYROPHOSPHATE'>EA2</scene> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene>
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<table><tr><td colspan='2'>[[2i6k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I6K FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2]
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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=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EA2:AMINOETHANOLPYROPHOSPHATE'>EA2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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}}
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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=2i6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i6k OCA], [https://pdbe.org/2i6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i6k RCSB], [https://www.ebi.ac.uk/pdbsum/2i6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i6k ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IDI1_HUMAN IDI1_HUMAN] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).<ref>PMID:8806705</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/i6/2i6k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2i6k ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Type I isopentenyl diphosphate (IPP): dimethylally diphosphate (DMAPP) isomerase is an essential enzyme in human isoprenoid biosynthetic pathway. It catalyzes isomerization of the carbon-carbon double bonds in IPP and DMAPP, which are the basic building blocks for the subsequent biosynthesis. We have determined two crystal structures of human IPP isomerase I (hIPPI) under different crystallization conditions. High similarity between structures of human and Escherichia coli IPP isomerases proves the conserved catalytic mechanism. Unexpectedly, one of the hIPPI structures contains a natural substrate analog ethanol amine pyrophosphate (EAPP). Based on this structure, a water molecule is proposed to be the direct proton donor for IPP and different conformations of IPP and DMAPP bound in the enzyme are also proposed. In addition, structures of human IPPI show a flexible N-terminal alpha-helix covering the active pocket and blocking the entrance, which is absent in E. coli IPPI. Besides, the active site conformation is not the same in the two hIPPI structures. Such difference leads to a hypothesis that substrate binding induces conformational change in the active site. The inhibition mechanism of high Mn(2+) concentrations is also discussed.
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'''Crystal structure of human type I IPP isomerase complexed with a substrate analog'''
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Crystal structures of human IPP isomerase: new insights into the catalytic mechanism.,Zhang C, Liu L, Xu H, Wei Z, Wang Y, Lin Y, Gong W J Mol Biol. 2007 Mar 9;366(5):1437-46. Epub 2006 Nov 3. PMID:17137593<ref>PMID:17137593</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2i6k" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Type I isopentenyl diphosphate (IPP): dimethylally diphosphate (DMAPP) isomerase is an essential enzyme in human isoprenoid biosynthetic pathway. It catalyzes isomerization of the carbon-carbon double bonds in IPP and DMAPP, which are the basic building blocks for the subsequent biosynthesis. We have determined two crystal structures of human IPP isomerase I (hIPPI) under different crystallization conditions. High similarity between structures of human and Escherichia coli IPP isomerases proves the conserved catalytic mechanism. Unexpectedly, one of the hIPPI structures contains a natural substrate analog ethanol amine pyrophosphate (EAPP). Based on this structure, a water molecule is proposed to be the direct proton donor for IPP and different conformations of IPP and DMAPP bound in the enzyme are also proposed. In addition, structures of human IPPI show a flexible N-terminal alpha-helix covering the active pocket and blocking the entrance, which is absent in E. coli IPPI. Besides, the active site conformation is not the same in the two hIPPI structures. Such difference leads to a hypothesis that substrate binding induces conformational change in the active site. The inhibition mechanism of high Mn(2+) concentrations is also discussed.
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*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
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== References ==
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==About this Structure==
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<references/>
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2I6K is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6K OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Crystal structures of human IPP isomerase: new insights into the catalytic mechanism., Zhang C, Liu L, Xu H, Wei Z, Wang Y, Lin Y, Gong W, J Mol Biol. 2007 Mar 9;366(5):1437-46. Epub 2006 Nov 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17137593 17137593]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Isopentenyl-diphosphate Delta-isomerase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Gong W]]
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[[Category: Gong, W.]]
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[[Category: Wei Z]]
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[[Category: Wei, Z.]]
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[[Category: Zhang C]]
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[[Category: Zhang, C.]]
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[[Category: ACY]]
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[[Category: EA2]]
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[[Category: MG]]
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[[Category: MN]]
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[[Category: fold]]
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[[Category: globular domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:26:03 2008''
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Current revision

Crystal structure of human type I IPP isomerase complexed with a substrate analog

PDB ID 2i6k

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