1p0n

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(New page: 200px<br /><applet load="1p0n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p0n, resolution 2.8&Aring;" /> '''IPP:DMAPP isomerase t...)
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[[Image:1p0n.jpg|left|200px]]<br /><applet load="1p0n" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1p0n, resolution 2.8&Aring;" />
 
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'''IPP:DMAPP isomerase type II, FMN complex'''<br />
 
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==Overview==
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==IPP:DMAPP isomerase type II, FMN complex==
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Two types of isopentenyl diphosphate:dimethylallyl diphosphate isomerases, (IDI) have been characterized at present. The long known IDI-1 is only, dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. Here, we report the first structure of an IDI-2 from, Bacillus subtilis at 1.9A resolution in the ligand-free form and of the, FMN-bound form at 2.8A resolution. The enzyme is an octamer that forms a, D4 symmetrical open, cage-like structure. The monomers of 45 kDa display a, classical TIM barrel fold. FMN is bound only with very moderate affinity, and is therefore completely lost during purification. However, the enzyme, can be reconstituted in the crystals by soaking with FMN. Three, glycine-rich sequence stretches that are characteristic for IDI-2, participate in FMN binding within the interior of the cage. Regions, harboring strictly conserved residues that are implicated in substrate, binding or catalysis remain largely disordered even in the presence of, FMN.
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<StructureSection load='1p0n' size='340' side='right'caption='[[1p0n]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1p0n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P0N FirstGlance]. <br>
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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]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></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=1p0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p0n OCA], [https://pdbe.org/1p0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p0n RCSB], [https://www.ebi.ac.uk/pdbsum/1p0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p0n ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IDI2_BACSU IDI2_BACSU] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity).
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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/p0/1p0n_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=1p0n 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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Two types of isopentenyl diphosphate:dimethylallyl diphosphate isomerases (IDI) have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. Here, we report the first structure of an IDI-2 from Bacillus subtilis at 1.9A resolution in the ligand-free form and of the FMN-bound form at 2.8A resolution. The enzyme is an octamer that forms a D4 symmetrical open, cage-like structure. The monomers of 45 kDa display a classical TIM barrel fold. FMN is bound only with very moderate affinity and is therefore completely lost during purification. However, the enzyme can be reconstituted in the crystals by soaking with FMN. Three glycine-rich sequence stretches that are characteristic for IDI-2 participate in FMN binding within the interior of the cage. Regions harboring strictly conserved residues that are implicated in substrate binding or catalysis remain largely disordered even in the presence of FMN.
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==About this Structure==
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Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis.,Steinbacher S, Kaiser J, Gerhardt S, Eisenreich W, Huber R, Bacher A, Rohdich F J Mol Biol. 2003 Jun 20;329(5):973-82. PMID:12798687<ref>PMID:12798687</ref>
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1P0N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1P0N OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis., Steinbacher S, Kaiser J, Gerhardt S, Eisenreich W, Huber R, Bacher A, Rohdich F, J Mol Biol. 2003 Jun 20;329(5):973-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12798687 12798687]
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</div>
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[[Category: Bacillus subtilis]]
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<div class="pdbe-citations 1p0n" style="background-color:#fffaf0;"></div>
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[[Category: Isopentenyl-diphosphate Delta-isomerase]]
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[[Category: Single protein]]
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[[Category: Bacher, A.]]
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[[Category: Eisenreich, W.]]
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[[Category: Gerhardt, S.]]
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[[Category: Huber, R.]]
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[[Category: Kaiser, J.]]
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[[Category: Rohdich, F.]]
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[[Category: Steinbacher, S.]]
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[[Category: FMN]]
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[[Category: dimethylallyl diphosphate]]
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[[Category: flavoprotein]]
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[[Category: isomerase]]
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[[Category: isopentenyl diphosphate]]
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[[Category: terpene biosynthesis]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:21:09 2007''
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==See Also==
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*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus subtilis]]
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[[Category: Large Structures]]
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[[Category: Bacher A]]
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[[Category: Eisenreich W]]
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[[Category: Gerhardt S]]
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[[Category: Huber R]]
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[[Category: Kaiser J]]
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[[Category: Rohdich F]]
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[[Category: Steinbacher S]]

Current revision

IPP:DMAPP isomerase type II, FMN complex

PDB ID 1p0n

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