1u3l: Difference between revisions

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-{{Seed}}
-[[Image:1u3l.png|left|200px]]
-<!--
+==IspF with Mg and CDP==
-The line below this paragraph, containing "STRUCTURE_1u3l", creates the "Structure Box" on the page.
+<StructureSection load='1u3l' size='340' side='right'caption='[[1u3l]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1u3l]] 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=1U3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U3L FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1u3l|  PDB=1u3l  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u3l OCA], [https://pdbe.org/1u3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u3l RCSB], [https://www.ebi.ac.uk/pdbsum/1u3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u3l 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/u3/1u3l_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=1u3l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===IspF with Mg and CDP===
+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:11829504<ref>PMID:11829504</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1u3l" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11829504}}, adds the Publication Abstract to the page
+*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11829504 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11829504}}
+__TOC__
+</StructureSection>
-==About this Structure==
-U3L is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U3L OCA].
-==Reference==
-<ref group="xtra">PMID:11829504</ref><references group="xtra"/>
-[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
 [[Category: Escherichia coli]]
-[[Category: Bacher, A.]]
+[[Category: Large Structures]]
-[[Category: Eisenreich, W.]]
+[[Category: Bacher A]]
-[[Category: Gerhardt, S.]]
+[[Category: Eisenreich W]]
-[[Category: Hechst, S.]]
+[[Category: Gerhardt S]]
-[[Category: Kaiser, J.]]
+[[Category: Hechst S]]
-[[Category: Rohdich, F.]]
+[[Category: Kaiser J]]
-[[Category: Steinbacher, S.]]
+[[Category: Rohdich F]]
-[[Category: Wungsintaweekul, J.]]
+[[Category: Steinbacher S]]
-[[Category: Lyase]]
+[[Category: Wungsintaweekul J]]
-[[Category: Mep pathway]]
-[[Category: Terpene biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:07:11 2009''