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| | <StructureSection load='7cpn' size='340' side='right'caption='[[7cpn]], [[Resolution|resolution]] 2.28Å' scene=''> | | <StructureSection load='7cpn' size='340' side='right'caption='[[7cpn]], [[Resolution|resolution]] 2.28Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7cpn]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thefy Thefy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CPN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CPN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7cpn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_fusca_YX Thermobifida fusca YX]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CPN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.28Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[7cpm|7cpm]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tfu_0853 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269800 THEFY])</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=7cpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cpn OCA], [https://pdbe.org/7cpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cpn RCSB], [https://www.ebi.ac.uk/pdbsum/7cpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cpn 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/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.88 2.5.1.88] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7cpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cpn OCA], [http://pdbe.org/7cpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cpn RCSB], [http://www.ebi.ac.uk/pdbsum/7cpn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cpn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPDP_THEFY DPDP_THEFY]] Catalyzes the synthesis of Z,E-mixed prenyl diphosphates by a condensation of isopentenyl diphosphate to an allylic diphosphate. It shows a large substrate specificity accepting dimethylallyl diphosphate (DMAPP), GPP, E,Efarnesyl diphosphate (FPP), E,E,E-geranylgeranyl diphosphate (GGPP), neryl diphosphate (Z-GPP), and (2Z,6E)-farnesyl diphosphate (Z,E-FPP) as allylic substrates. The enzyme exhibits the highest activity when Z,E-FPP is employed as an allylic substrate. The major product is dodecaprenyl diphosphate (C60) under every allylic substrate conditions, but the enzyme is also able to synthesize even C70 prenyl diphosphate as the maximum chain-length product.<ref>PMID:19447338</ref> | + | [https://www.uniprot.org/uniprot/DPDP_THEFY DPDP_THEFY] Catalyzes the synthesis of Z,E-mixed prenyl diphosphates by a condensation of isopentenyl diphosphate to an allylic diphosphate. It shows a large substrate specificity accepting dimethylallyl diphosphate (DMAPP), GPP, E,Efarnesyl diphosphate (FPP), E,E,E-geranylgeranyl diphosphate (GGPP), neryl diphosphate (Z-GPP), and (2Z,6E)-farnesyl diphosphate (Z,E-FPP) as allylic substrates. The enzyme exhibits the highest activity when Z,E-FPP is employed as an allylic substrate. The major product is dodecaprenyl diphosphate (C60) under every allylic substrate conditions, but the enzyme is also able to synthesize even C70 prenyl diphosphate as the maximum chain-length product.<ref>PMID:19447338</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thefy]] | + | [[Category: Thermobifida fusca YX]] |
| - | [[Category: Transferase]]
| + | [[Category: Ambo T]] |
| - | [[Category: Ambo, T]] | + | [[Category: Koyama T]] |
| - | [[Category: Koyama, T]] | + | [[Category: Kurokawa H]] |
| - | [[Category: Kurokawa, H]] | + | [[Category: Takahasi S]] |
| - | [[Category: Takahasi, S]] | + | |
| - | [[Category: Prenyltransferase]]
| + | |
| Structural highlights
Function
DPDP_THEFY Catalyzes the synthesis of Z,E-mixed prenyl diphosphates by a condensation of isopentenyl diphosphate to an allylic diphosphate. It shows a large substrate specificity accepting dimethylallyl diphosphate (DMAPP), GPP, E,Efarnesyl diphosphate (FPP), E,E,E-geranylgeranyl diphosphate (GGPP), neryl diphosphate (Z-GPP), and (2Z,6E)-farnesyl diphosphate (Z,E-FPP) as allylic substrates. The enzyme exhibits the highest activity when Z,E-FPP is employed as an allylic substrate. The major product is dodecaprenyl diphosphate (C60) under every allylic substrate conditions, but the enzyme is also able to synthesize even C70 prenyl diphosphate as the maximum chain-length product.[1]
Publication Abstract from PubMed
cis-Prenyltransferases (cis-PTs) catalyze consecutive condensations of isopentenyl diphosphate to an allylic diphosphate acceptor to produce a linear polyprenyl diphosphate of designated length. Dimer formation is a prerequisite for cis-PTs to catalyze all cis-prenyl condensation reactions. The structure-function relationship of a conserved C-terminal RXG motif in cis-PTs that forms inter-subunit interactions and has a role in catalytic activity has attracted much attention. Here, we solved the crystal structure of a medium-chain cis-PT from Thermobifida fusca that produces dodecaprenyl diphosphate as a polyprenoid glycan carrier for cell wall synthesis. The structure revealed a characteristic dimeric architecture of cis-PTs in which a rigidified RXG motif of one monomer formed inter-subunit hydrogen bonds with the catalytic site of the other monomer, while the RXG motif of the latter remained flexible. Careful analyses suggested the existence of a possible long-range negative cooperativity between the two catalytic sites on the two monomeric subunits that allowed the binding of one subunit to stabilize the formation of the enzyme-substrate ternary complex and facilitated the release of Mg-PPi and subsequent intra-molecular translocation at the counter subunit so that the condensation reaction could occur in consecutive cycles. The current structure reveals the dynamic nature of the RXG motif and provides a rationale for pursuing further investigations to elucidate the inter-subunit cooperativity of cis-PTs.
Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity.,Kurokawa H, Ambo T, Takahashi S, Koyama T Biochem Biophys Res Commun. 2020 Nov 12;532(3):459-465. doi:, 10.1016/j.bbrc.2020.08.062. Epub 2020 Sep 4. PMID:32892948[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ambo T, Noike M, Kurokawa H, Koyama T. Cloning and functional analysis of cis-prenyltransferase from Thermobifida fusca. J Biosci Bioeng. 2009 Jun;107(6):620-2. doi: 10.1016/j.jbiosc.2009.02.006. PMID:19447338 doi:http://dx.doi.org/10.1016/j.jbiosc.2009.02.006
- ↑ Kurokawa H, Ambo T, Takahashi S, Koyama T. Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem Biophys Res Commun. 2020 Nov 12;532(3):459-465. doi:, 10.1016/j.bbrc.2020.08.062. Epub 2020 Sep 4. PMID:32892948 doi:http://dx.doi.org/10.1016/j.bbrc.2020.08.062
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