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1knj

From Proteopedia

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[[Image:1knj.gif|left|200px]]<br /><applet load="1knj" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1knj, resolution 2.80&Aring;" />
 
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'''Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+'''<br />
 
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==Overview==
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==Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+==
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The enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to MECDP, a highly unusual cyclodiphosphate-containing intermediate on the mevalonate-independent pathway to isopentenyl diphosphate and dimethylallyl diphosphate. We now report two x-ray crystal structures of MECDP synthase refined to 2.8-A resolution. The first structure contains a bound Mn(2+) cation, and the second structure contains CMP, MECDP, and Mn(2+). The protein adopts a homotrimeric quaternary structure built around a central hydrophobic cavity and three externally facing active sites. Each of these active sites is located between two adjacent monomers. A tetrahedrally arranged transition metal binding site, potentially occupied by Mn(2+), sits at the base of the active site cleft. A phosphate oxygen of MECDP and the side chains of Asp(8), His(10), and His(42) occupy the metal ion coordination sphere. These structures reveal for the first time the structural determinants underlying substrate, product, and Mn(2+) recognition and the likely catalytic mechanism accompanying the biosynthesis of the cyclodiphosphate-containing isoprenoid precursor, MECDP.
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<StructureSection load='1knj' size='340' side='right'caption='[[1knj]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1knj]] 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=1KNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNJ 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=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=CDI:2C-METHYL-D-ERYTHRITOL+2,4-CYCLODIPHOSPHATE'>CDI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1knj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1knj OCA], [https://pdbe.org/1knj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1knj RCSB], [https://www.ebi.ac.uk/pdbsum/1knj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1knj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/kn/1knj_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=1knj ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KNJ 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=MN:'>MN</scene>, <scene name='pdbligand=C5P:'>C5P</scene> and <scene name='pdbligand=CDI:'>CDI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNJ OCA].
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*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway., Richard SB, Ferrer JL, Bowman ME, Lillo AM, Tetzlaff CN, Cane DE, Noel JP, J Biol Chem. 2002 Mar 8;277(10):8667-72. Epub 2002 Jan 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11786530 11786530]
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bowman, M E.]]
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[[Category: Bowman ME]]
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[[Category: Cane, D E.]]
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[[Category: Cane DE]]
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[[Category: Ferrer, J L.]]
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[[Category: Ferrer JL]]
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[[Category: Lillo, A M.]]
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[[Category: Lillo AM]]
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[[Category: Noel, J P.]]
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[[Category: Noel JP]]
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[[Category: Richard, S B.]]
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[[Category: Richard SB]]
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[[Category: Tetzlaff, C N.]]
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[[Category: Tetzlaff CN]]
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[[Category: C5P]]
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[[Category: CDI]]
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[[Category: MN]]
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[[Category: 2-c-methyl-d-erythritol-2]]
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[[Category: 4-cyclodiphosphate synthase]]
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[[Category: cyclodiphosphate]]
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[[Category: deoxyxylulose/methyl-erythritol-phosphate pathway]]
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[[Category: isoprenoids]]
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[[Category: ispf]]
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[[Category: mecdp]]
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[[Category: mep]]
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[[Category: ygbb]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:36:00 2008''
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Current revision

Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+

PDB ID 1knj

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