3b05: Difference between revisions

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 ==Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP at 2.2A resolution.==
-<StructureSection load='3b05' size='340' side='right' caption='[[3b05]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3b05' size='340' side='right'caption='[[3b05]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b05]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51178 Atcc 51178]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B05 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B05 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b05]] 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=3B05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B05 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b03|3b03]], [[3b04|3b04]], [[3b06|3b06]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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 ATCC 51178])</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=3b05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b05 OCA], [https://pdbe.org/3b05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b05 RCSB], [https://www.ebi.ac.uk/pdbsum/3b05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b05 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=3b05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b05 OCA], [http://pdbe.org/3b05 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b05 RCSB], [http://www.ebi.ac.uk/pdbsum/3b05 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b05 ProSAT]</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>
-<div class="pdbe-citations 3b05" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 28: / Line 17: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 51178]]
+[[Category: Large Structures]]
-[[Category: Isopentenyl-diphosphate Delta-isomerase]]
+[[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: Ipp]]
-[[Category: Isomerase]]
-[[Category: Isopentenyl diphosphate isomerase]]
-[[Category: Type 2]]