2j1p
From Proteopedia
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| - | == | + | |
| - | <StructureSection load='2j1p' size='340' side='right' caption='[[2j1p]], [[Resolution|resolution]] 1.80Å' scene=''> | + | ==Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP== |
| + | <StructureSection load='2j1p' size='340' side='right'caption='[[2j1p]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | [[2j1p]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2j1p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinapis_alba Sinapis alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J1P FirstGlance]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GRG:GERANYLGERANYL+DIPHOSPHATE'>GRG</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene>< | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GRG:GERANYLGERANYL+DIPHOSPHATE'>GRG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr> | |
| - | <b> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j1p OCA], [https://pdbe.org/2j1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j1p RCSB], [https://www.ebi.ac.uk/pdbsum/2j1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j1p ProSAT]</span></td></tr> |
| - | + | </table> | |
| - | + | == Function == | |
| + | [https://www.uniprot.org/uniprot/GGPPS_SINAL GGPPS_SINAL] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| - | [[Image:Consurf_key_small.gif|right]] | + | [[Image:Consurf_key_small.gif|200px|right]] |
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j1/2j1p_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j1/2j1p_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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=2j1p ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
The crystal structure of the geranylgeranyl diphosphate synthase from Sinapis alba (mustard) has been solved in two crystal forms at 1.8 and 2.0 A resolutions. In one of these forms, the dimeric enzyme binds one molecule of the final product geranylgeranyl diphosphate in one subunit. The chainfold of the enzyme corresponds to that of other members of the farnesyl diphosphate synthase family. Whereas the binding modes of the two substrates dimethylallyl diphosphate and isopentenyl diphosphate at the allyl and isopentenyl sites, respectively, have been established with other members of the family, the complex structure presented reveals for the first time the binding mode of a reaction product at the isopentenyl site. The binding geometry of substrates and product in conjunction with the protein environment and the established chemistry of the reaction provide a clear picture of the reaction steps and atom displacements. Moreover, a comparison with a ligated homologous structure outlined an appreciable induced fit: helix alpha8 and its environment undergo a large conformational change when either the substrate dimethylallyl diphosphate or an analogue is bound to the allyl site; only a minor conformational change occurs when the other substrate isopentenyl diphosphate or the product is bound to the isopentenyl site. | The crystal structure of the geranylgeranyl diphosphate synthase from Sinapis alba (mustard) has been solved in two crystal forms at 1.8 and 2.0 A resolutions. In one of these forms, the dimeric enzyme binds one molecule of the final product geranylgeranyl diphosphate in one subunit. The chainfold of the enzyme corresponds to that of other members of the farnesyl diphosphate synthase family. Whereas the binding modes of the two substrates dimethylallyl diphosphate and isopentenyl diphosphate at the allyl and isopentenyl sites, respectively, have been established with other members of the family, the complex structure presented reveals for the first time the binding mode of a reaction product at the isopentenyl site. The binding geometry of substrates and product in conjunction with the protein environment and the established chemistry of the reaction provide a clear picture of the reaction steps and atom displacements. Moreover, a comparison with a ligated homologous structure outlined an appreciable induced fit: helix alpha8 and its environment undergo a large conformational change when either the substrate dimethylallyl diphosphate or an analogue is bound to the allyl site; only a minor conformational change occurs when the other substrate isopentenyl diphosphate or the product is bound to the isopentenyl site. | ||
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Structure and reaction geometry of geranylgeranyl diphosphate synthase from Sinapis alba.,Kloer DP, Welsch R, Beyer P, Schulz GE Biochemistry. 2006 Dec 26;45(51):15197-204. Epub 2006 Dec 1. PMID:17176041<ref>PMID:17176041</ref> | Structure and reaction geometry of geranylgeranyl diphosphate synthase from Sinapis alba.,Kloer DP, Welsch R, Beyer P, Schulz GE Biochemistry. 2006 Dec 26;45(51):15197-204. Epub 2006 Dec 1. PMID:17176041<ref>PMID:17176041</ref> | ||
| - | From | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> | ||
| + | <div class="pdbe-citations 2j1p" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Geranylgeranyl pyrophosphate synthase 3D structures|Geranylgeranyl pyrophosphate synthase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Sinapis alba]] | [[Category: Sinapis alba]] | ||
| - | [[Category: Beyer | + | [[Category: Beyer P]] |
| - | [[Category: Kloer | + | [[Category: Kloer DP]] |
| - | [[Category: Schulz | + | [[Category: Schulz GE]] |
| - | [[Category: Welsch | + | [[Category: Welsch R]] |
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Current revision
Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP
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