|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6onm' size='340' side='right'caption='[[6onm]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='6onm' size='340' side='right'caption='[[6onm]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6onm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Citsi Citsi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ONM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ONM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6onm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrus_sinensis Citrus sinensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ONM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ONM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MWG:(3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl+trihydrogen+diphosphate'>MWG</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]] 2.7Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(R)-limonene_synthase (R)-limonene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.20 4.2.3.20] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MWG:(3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl+trihydrogen+diphosphate'>MWG</scene></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=6onm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6onm OCA], [http://pdbe.org/6onm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6onm RCSB], [http://www.ebi.ac.uk/pdbsum/6onm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6onm ProSAT]</span></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=6onm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6onm OCA], [https://pdbe.org/6onm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6onm RCSB], [https://www.ebi.ac.uk/pdbsum/6onm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6onm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RLC1_CITSI RLC1_CITSI] Catalyzes the conversion of geranyl diphosphate to (+)-(4R)-limonene (PubMed:28272875, PubMed:28272876). Produces exclusively the (+)-enantiomer (PubMed:28272875). Can use neryl diphosphate as substrate (PubMed:28272876). Has no activity with farnesyl diphosphate (PubMed:28272875).<ref>PMID:28272875</ref> <ref>PMID:28272876</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Citsi]] | + | [[Category: Citrus sinensis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kumar, R Prem]] | + | [[Category: Morehouse BR]] |
| - | [[Category: Morehouse, B R]] | + | [[Category: Oprian DD]] |
| - | [[Category: Oprian, D D]] | + | [[Category: Prem Kumar R]] |
| - | [[Category: Yu, Q]] | + | [[Category: Yu Q]] |
| - | [[Category: Enantiomer]]
| + | |
| - | [[Category: Fluoro analog]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metal binding]]
| + | |
| - | [[Category: Monoterpene]]
| + | |
| - | [[Category: Terpene synthase]]
| + | |
| - | [[Category: Terpene synthase fold]]
| + | |
| Structural highlights
Function
RLC1_CITSI Catalyzes the conversion of geranyl diphosphate to (+)-(4R)-limonene (PubMed:28272875, PubMed:28272876). Produces exclusively the (+)-enantiomer (PubMed:28272875). Can use neryl diphosphate as substrate (PubMed:28272876). Has no activity with farnesyl diphosphate (PubMed:28272875).[1] [2]
Publication Abstract from PubMed
Linalyl diphosphate (LPP) is the postulated intermediate in the enzymatic cyclization of monoterpenes catalyzed by terpene synthases. LPP is considered an obligate intermediate due to the conformationally restrictive trans-C2-C3 double bond of the substrate, geranyl diphosphate (GPP), which precludes the proper positioning of carbons C1 and C6 to enable cyclization. However, because of the complexity of potential carbocation-mediated rearrangements in these enzymatic reactions, it has proven difficult to directly demonstrate the formation of LPP despite significant efforts. Here we synthesized a fluorinated substrate analog, 8,9-difluorogeranyl diphosphate (DFGPP), which is designed to allow initial ionization/isomerization and form the fluorinated equivalent of LPP (DFLPP) while preventing the subsequent ionization/cyclization to produce the alpha-terpinyl cation. Steady-state kinetic studies with the model enzyme (+)-limonene synthase (LS) under catalytic conditions show that the cyclization of DFGPP is completely blocked and a single linear product, difluoromyrcene, is produced. When crystals of apo-LS are soaked with DFGPP under conditions limiting turnover of the enzyme, we show, using X-ray crystallography, that DFLPP is produced in the enzyme active site and trapped in the crystals. Clear electron density is observed in the active site of the enzyme, but it cannot be appropriately fit with a model for the DFGPP substrate analog, whereas it can accommodate an extended conformation of DFLPP. This result supports the current model for monoterpene cyclization by providing direct evidence of LPP as an intermediate.
Direct Evidence of an Enzyme-Generated LPP Intermediate in (+)-Limonene Synthase Using a Fluorinated GPP Substrate Analog.,Morehouse BR, Kumar RP, Matos JO, Yu Q, Bannister A, Malik K, Temme JS, Krauss IJ, Oprian DD ACS Chem Biol. 2019 Sep 20;14(9):2035-2043. doi: 10.1021/acschembio.9b00514. Epub, 2019 Sep 4. PMID:31433159[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Morehouse BR, Kumar RP, Matos JO, Olsen SN, Entova S, Oprian DD. Functional and Structural Characterization of a (+)-Limonene Synthase from Citrus sinensis. Biochemistry. 2017 Mar 15. doi: 10.1021/acs.biochem.7b00143. PMID:28272875 doi:http://dx.doi.org/10.1021/acs.biochem.7b00143
- ↑ Kumar RP, Morehouse BR, Matos JO, Malik K, Lin H, Krauss IJ, Oprian DD. Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues. Biochemistry. 2017 Mar 15. doi: 10.1021/acs.biochem.7b00144. PMID:28272876 doi:http://dx.doi.org/10.1021/acs.biochem.7b00144
- ↑ Morehouse BR, Kumar RP, Matos JO, Yu Q, Bannister A, Malik K, Temme JS, Krauss IJ, Oprian DD. Direct Evidence of an Enzyme-Generated LPP Intermediate in (+)-Limonene Synthase Using a Fluorinated GPP Substrate Analog. ACS Chem Biol. 2019 Sep 20;14(9):2035-2043. doi: 10.1021/acschembio.9b00514. Epub, 2019 Sep 4. PMID:31433159 doi:http://dx.doi.org/10.1021/acschembio.9b00514
|
