1u3p: Difference between revisions

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-[[Image:1u3p.jpg|left|200px]]<br /><applet load="1u3p" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1u3p, resolution 2.85&Aring;" />
-'''IspF native'''<br />
-==Overview==
+==IspF native==
-Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The non-mevalonate pathway is present in many bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum and in the plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised as promising drug targets. We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction. The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2-phosphate group on the beta-phosphate.
+<StructureSection load='1u3p' size='340' side='right'caption='[[1u3p]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1u3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U3P FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1u3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u3p OCA], [https://pdbe.org/1u3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u3p RCSB], [https://www.ebi.ac.uk/pdbsum/1u3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u3p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ISPF_ECOLI ISPF_ECOLI] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.<ref>PMID:10694574</ref> <ref>PMID:22839733</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u3/1u3p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1u3p ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-U3P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U3P OCA].
+*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids., Steinbacher S, Kaiser J, Wungsintaweekul J, Hecht S, Eisenreich W, Gerhardt S, Bacher A, Rohdich F, J Mol Biol. 2002 Feb 8;316(1):79-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11829504 11829504]
+__TOC__
-[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bacher, A.]]
+[[Category: Bacher A]]
-[[Category: Eisenreich, W.]]
+[[Category: Eisenreich W]]
-[[Category: Gerhardt, S.]]
+[[Category: Gerhardt S]]
-[[Category: Hecht, S.]]
+[[Category: Hecht S]]
-[[Category: Kaiser, J.]]
+[[Category: Kaiser J]]
-[[Category: Rohdich, F.]]
+[[Category: Rohdich F]]
-[[Category: Steinbacher, S.]]
+[[Category: Steinbacher S]]
-[[Category: Wungsintaweekul, J.]]
+[[Category: Wungsintaweekul J]]
-[[Category: ZN]]
-[[Category: lyase]]
-[[Category: mep pathway]]
-[[Category: terpene biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:20:24 2008''