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| | <StructureSection load='6jo3' size='340' side='right'caption='[[6jo3]], [[Resolution|resolution]] 2.35Å' scene=''> | | <StructureSection load='6jo3' size='340' side='right'caption='[[6jo3]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jo3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Theac Theac]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5b69 5b69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JO3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jo3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum_DSM_1728 Thermoplasma acidophilum DSM 1728]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5b69 5b69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JO3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1GP:SN-GLYCEROL-1-PHOSPHATE'>1GP</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]] 2.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mm1|4mm1]], [[2f6x|2f6x]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GP:SN-GLYCEROL-1-PHOSPHATE'>1GP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0995 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273075 THEAC])</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=6jo3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jo3 OCA], [https://pdbe.org/6jo3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jo3 RCSB], [https://www.ebi.ac.uk/pdbsum/6jo3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jo3 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/Phosphoglycerol_geranylgeranyltransferase Phosphoglycerol geranylgeranyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.41 2.5.1.41] </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=6jo3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jo3 OCA], [http://pdbe.org/6jo3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jo3 RCSB], [http://www.ebi.ac.uk/pdbsum/6jo3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jo3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GGGPS_THEAC GGGPS_THEAC]] Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. Cannot use sn-glycerol-3-phosphate (G3P) as substrate.<ref>PMID:12801917</ref> <ref>PMID:24684232</ref> | + | [https://www.uniprot.org/uniprot/GGGPS_THEAC GGGPS_THEAC] Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. Cannot use sn-glycerol-3-phosphate (G3P) as substrate.<ref>PMID:12801917</ref> <ref>PMID:24684232</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | (S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35 A resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (alpha3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the beta2-alpha2, alpha3* and alpha5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS. |
| | + | |
| | + | Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate.,Nemoto N, Miyazono KI, Tanokura M, Yamagishi A Acta Crystallogr F Struct Biol Commun. 2019 Jul 1;75(Pt 7):470-479. doi:, 10.1107/S2053230X19007453. Epub 2019 Jun 17. PMID:31282866<ref>PMID:31282866</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 6jo3" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Phosphoglycerol geranylgeranyltransferase]] | + | [[Category: Thermoplasma acidophilum DSM 1728]] |
| - | [[Category: Theac]]
| + | [[Category: Miyazono K]] |
| - | [[Category: Miyazono, K]] | + | [[Category: Nemoto N]] |
| - | [[Category: Nemoto, N]] | + | [[Category: Tanokura M]] |
| - | [[Category: Tanokura, M]] | + | [[Category: Yamagishi A]] |
| - | [[Category: Yamagishi, A]] | + | |
| - | [[Category: Archaea]]
| + | |
| - | [[Category: Ether lipid]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Thermoplasma]]
| + | |
| - | [[Category: Transferase]]
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| Structural highlights
Function
GGGPS_THEAC Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. Cannot use sn-glycerol-3-phosphate (G3P) as substrate.[1] [2]
Publication Abstract from PubMed
(S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35 A resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (alpha3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the beta2-alpha2, alpha3* and alpha5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS.
Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate.,Nemoto N, Miyazono KI, Tanokura M, Yamagishi A Acta Crystallogr F Struct Biol Commun. 2019 Jul 1;75(Pt 7):470-479. doi:, 10.1107/S2053230X19007453. Epub 2019 Jun 17. PMID:31282866[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nemoto N, Oshima T, Yamagishi A. Purification and characterization of geranylgeranylglyceryl phosphate synthase from a thermoacidophilic archaeon, Thermoplasma acidophilum. J Biochem. 2003 May;133(5):651-7. PMID:12801917
- ↑ Peterhoff D, Beer B, Rajendran C, Kumpula EP, Kapetaniou E, Guldan H, Wierenga RK, Sterner R, Babinger P. A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization. Mol Microbiol. 2014 May;92(4):885-99. doi: 10.1111/mmi.12596. Epub 2014 Apr 16. PMID:24684232 doi:http://dx.doi.org/10.1111/mmi.12596
- ↑ Nemoto N, Miyazono KI, Tanokura M, Yamagishi A. Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate. Acta Crystallogr F Struct Biol Commun. 2019 Jul 1;75(Pt 7):470-479. doi:, 10.1107/S2053230X19007453. Epub 2019 Jun 17. PMID:31282866 doi:http://dx.doi.org/10.1107/S2053230X19007453
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