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| | <StructureSection load='2i6k' size='340' side='right'caption='[[2i6k]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='2i6k' size='340' side='right'caption='[[2i6k]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2i6k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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> | + | <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> |
| - | </td></tr><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></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
| + | <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> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ewq|2ewq]], [[2dho|2dho]]</div></td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2] </span></td></tr>
| + | |
| | <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> | | <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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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>
| + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Isopentenyl-diphosphate Delta-isomerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Gong, W]] | + | [[Category: Gong W]] |
| - | [[Category: Wei, Z]] | + | [[Category: Wei Z]] |
| - | [[Category: Zhang, C]] | + | [[Category: Zhang C]] |
| - | [[Category: Fold]]
| + | |
| - | [[Category: Globular domain]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
2i6k is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
IDI1_HUMAN Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hahn FM, Xuan JW, Chambers AF, Poulter CD. Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization. Arch Biochem Biophys. 1996 Aug 1;332(1):30-4. PMID:8806705 doi:http://dx.doi.org/S0003-9861(96)90312-4
- ↑ Zhang C, Liu L, Xu H, Wei Z, Wang Y, Lin Y, Gong W. Crystal structures of human IPP isomerase: new insights into the catalytic mechanism. J Mol Biol. 2007 Mar 9;366(5):1437-46. Epub 2006 Nov 3. PMID:17137593 doi:10.1016/j.jmb.2006.10.092
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