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3b04

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Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oIPP.

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Categories: Large Structures | Saccharolobus shibatae | Hemmi H | Nagai T | Unno H

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 ==Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oIPP.==
-<StructureSection load='3b04' size='340' side='right' caption='[[3b04]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3b04' size='340' side='right'caption='[[3b04]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b04]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_shibatae Sulfolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B04 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B04 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b04]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae Saccharolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B04 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OOP:1-DEOXY-1-[(4AR)-4A-[(2R)-1-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLIDENEPENTAN-2-YL]-7,8-DIMETHYL-2,4-DIOXO-3,4,4A,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL'>OOP</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b03|3b03]], [[3b05|3b05]], [[3b06|3b06]]</td></tr>
+<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=OOP:1-DEOXY-1-[(4AR)-4A-[(2R)-1-HYDROXY-5-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLIDENEPENTAN-2-YL]-7,8-DIMETHYL-2,4-DIOXO-3,4,4A,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL'>OOP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fni, idi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 Sulfolobus shibatae])</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=3b04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b04 OCA], [https://pdbe.org/3b04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b04 RCSB], [https://www.ebi.ac.uk/pdbsum/3b04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b04 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b04 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b04 RCSB], [http://www.ebi.ac.uk/pdbsum/3b04 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IDI2_SULSH IDI2_SULSH]] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity).
+[https://www.uniprot.org/uniprot/IDI2_SACSH IDI2_SACSH] Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354]<ref>PMID:19158086</ref> <ref>PMID:22158896</ref> <ref>PMID:22505674</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Evidence for an unusual catalysis of protonation/deprotonation by a reduced flavin mononucleotide cofactor is presented for type-2 isopentenyl diphosphate isomerase (IDI-2), which catalyzes isomerization of the two fundamental building blocks of isoprenoid biosynthesis, isopentenyl diphosphate and dimethylallyl diphosphate. The covalent adducts formed between irreversible mechanism-based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxiranyl-3-buten-1-yl diphosphate, and the flavin cofactor were investigated by X-ray crystallography and UV-visible spectroscopy. Both the crystal structures of IDI-2 binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5, which had been proposed previously. In addition, the high-resolution crystal structures of IDI-2-substrate complexes and the kinetic studies of new mutants confirmed that only the flavin cofactor can catalyze protonation of the substrates and suggest that N5 of flavin is most likely to be involved in proton transfer. These data provide support for a mechanism where the reduced flavin cofactor acts as a general acid/base catalyst and helps stabilize the carbocationic intermediate formed by protonation.
-Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.,Nagai T, Unno H, Janczak MW, Yoshimura T, Poulter CD, Hemmi H Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20461-6. Epub 2011 Dec 7. PMID:22158896<ref>PMID:22158896</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
 *[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
-*[[Nucleoprotein|Nucleoprotein]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Isopentenyl-diphosphate Delta-isomerase]]
+[[Category: Large Structures]]
-[[Category: Sulfolobus shibatae]]
+[[Category: Saccharolobus shibatae]]
-[[Category: Hemmi, H]]
+[[Category: Hemmi H]]
-[[Category: Nagai, T]]
+[[Category: Nagai T]]
-[[Category: Unno, H]]
+[[Category: Unno H]]
-[[Category: Fmn]]
-[[Category: Idi]]
-[[Category: Isomerase]]
-[[Category: Isopentenyl diphosphate isomerase]]
-[[Category: Oipp]]
-[[Category: Type 2]]

3b04

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Current revision

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oIPP.

Structural highlights

Function

See Also

References

Contents

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