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| | ==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis== | | ==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis== |
| - | <StructureSection load='5iwx' size='340' side='right' caption='[[5iwx]], [[Resolution|resolution]] 1.99Å' scene=''> | + | <StructureSection load='5iwx' size='340' side='right'caption='[[5iwx]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5iwx]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IWX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5iwx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IWX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.99Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iwy|5iwy]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ispF, yacN, BSU00910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5iwx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwx OCA], [https://pdbe.org/5iwx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iwx RCSB], [https://www.ebi.ac.uk/pdbsum/5iwx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwx 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/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] </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=5iwx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwx OCA], [http://pdbe.org/5iwx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwx RCSB], [http://www.ebi.ac.uk/pdbsum/5iwx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU]] 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).<ref>PMID:17458547</ref> | + | [https://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU] 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).<ref>PMID:17458547</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5iwx" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5iwx" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[MECDP synthase 3D structures|MECDP synthase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Bacsu]] | + | [[Category: Large Structures]] |
| - | [[Category: Jin, Y]] | + | [[Category: Jin Y]] |
| - | [[Category: Liu, Z C]] | + | [[Category: Liu ZC]] |
| - | [[Category: Wang, G G]] | + | [[Category: Wang GG]] |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
ISPF_BACSU 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).[1]
Publication Abstract from PubMed
2-C-methyl-d-erythritol 2, 4-cyclodiphosphate synthase (IspF) is a key enzyme in the 2-C-Methyl-d-erythritol-4-phosphate (MEP) pathway of isoprenoid biosynthesis. This enzyme catalyzes the 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate (CDPME2P) to 2-C-methyl-d-erythritol 2, 4-cyclodiphosphate (MEcDP) with concomitant release of cytidine 5'-diphospate (cytosine monophosphate) (CMP). Bacillus subtilis is a potential host cell for the production of isoprenoids, but few studies are performed on the key enzymes of MEP pathway in B. subtilis In this work, the high resolution crystal structures of IspF in native and complex with CMP from B. subtilis have been determinated. Structural comparisons indicate that there is a looser packing of the subunits of IspF in B. subtilis , whereas the solvent accessible surface of its active pockets is smaller than that in Escherichia coli. Meanwhile, the protein-protein associations of 2-C-Methyl-d-erythritol-4-phosphatecytidyltransferase (IspD), 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase (IspE) and IspF from B. subtilis and E. coli , which catalyze three consecutive steps in the MEP pathway, are analyzed by native gel shift and size exclusion chromatography methods. The data here shows that protein complex assembly is not detectable. These results will be useful for isoprenoid biosynthesis by metabolic engineering.
Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway.,Liu Z, Jin Y, Liu W, Tao Y, Wang G Biosci Rep. 2018 Jan 15. pii: BSR20171370. doi: 10.1042/BSR20171370. PMID:29335298[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Julsing MK, Rijpkema M, Woerdenbag HJ, Quax WJ, Kayser O. Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis. Appl Microbiol Biotechnol. 2007 Jul;75(6):1377-84. Epub 2007 Apr 26. PMID:17458547 doi:http://dx.doi.org/10.1007/s00253-007-0953-5
- ↑ Liu Z, Jin Y, Liu W, Tao Y, Wang G. Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway. Biosci Rep. 2018 Jan 15. pii: BSR20171370. doi: 10.1042/BSR20171370. PMID:29335298 doi:http://dx.doi.org/10.1042/BSR20171370
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