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==Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)== | |||
<StructureSection load='8x35' size='340' side='right'caption='[[8x35]], [[Resolution|resolution]] 1.92Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8x35]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8X35 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8X35 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=8x35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8x35 OCA], [https://pdbe.org/8x35 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8x35 RCSB], [https://www.ebi.ac.uk/pdbsum/8x35 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8x35 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CPT1_SOLLC CPT1_SOLLC] Uses dimethylallyl diphosphate and isopentenyl diphosphate to catalyze the cis-prenyl chain elongation and produce the 10 carbon product neryl diphosphate.<ref>PMID:19487664</ref> <ref>PMID:23134568</ref> <ref>PMID:23757397</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Neryl diphosphate (C(10)) synthase (NDPS1), a homodimeric soluble cis-prenyltransferase from tomato, contains four disulfide bonds, including two inter-subunit S-S bonds in the N-terminal region. Mutagenesis studies demonstrated that the S-S bond formation affects not only the stability of the dimer but also the catalytic efficiency of NDPS1. Structural polymorphs in the crystal structures of NDPS1 complexed with its substrate and substrate analog were identified by employing massive data collections and hierarchical clustering analysis. Heterogeneity of the C-terminal region, including the conserved RXG motifs, was observed in addition to the polymorphs of the binding mode of the ligands. One of the RXG motifs covers the active site with an elongated random coil when the ligands are well-ordered. Conversely, the other RXG motif was located away from the active site with a helical structure. The heterogeneous C-terminal regions suggest alternating structural transitions of the RXG motifs that result in closed and open states of the active sites. Site-directed mutagenesis studies demonstrated that the conserved glycine residue cannot be replaced. We propose that the putative structural transitions of the order/disorder of N-terminal regions and the closed/open states of C-terminal regions may cooperate and be important for the catalytic mechanism of NDPS1. | |||
Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.,Imaizumi R, Matsuura H, Yanai T, Takeshita K, Misawa S, Yamaguchi H, Sakai N, Miyagi-Inoue Y, Suenaga-Hiromori M, Waki T, Kataoka K, Nakayama T, Yamamoto M, Takahashi S, Yamashita S Chembiochem. 2024 Apr 2;25(7):e202300796. doi: 10.1002/cbic.202300796. Epub 2024 , Jan 29. PMID:38225831<ref>PMID:38225831</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8x35" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Nakayama | [[Category: Large Structures]] | ||
[[Category: | [[Category: Solanum lycopersicum]] | ||
[[Category: | [[Category: Imaizumi R]] | ||
[[Category: | [[Category: Kataoka K]] | ||
[[Category: | [[Category: Matsuura H]] | ||
[[Category: | [[Category: Misawa S]] | ||
[[Category: | [[Category: Miyagi-Inoue Y]] | ||
[[Category: | [[Category: Nakayama T]] | ||
[[Category: Yanai | [[Category: Sakai N]] | ||
[[Category: Suenaga-Hiromori M]] | |||
[[Category: Takahashi S]] | |||
[[Category: Takeshita K]] | |||
[[Category: Yamaguchi H]] | |||
[[Category: Yamamoto M]] | |||
[[Category: Yamashita S]] | |||
[[Category: Yanai T]] | |||
Latest revision as of 15:41, 23 October 2024
Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)
Structural highlights
FunctionCPT1_SOLLC Uses dimethylallyl diphosphate and isopentenyl diphosphate to catalyze the cis-prenyl chain elongation and produce the 10 carbon product neryl diphosphate.[1] [2] [3] Publication Abstract from PubMedNeryl diphosphate (C(10)) synthase (NDPS1), a homodimeric soluble cis-prenyltransferase from tomato, contains four disulfide bonds, including two inter-subunit S-S bonds in the N-terminal region. Mutagenesis studies demonstrated that the S-S bond formation affects not only the stability of the dimer but also the catalytic efficiency of NDPS1. Structural polymorphs in the crystal structures of NDPS1 complexed with its substrate and substrate analog were identified by employing massive data collections and hierarchical clustering analysis. Heterogeneity of the C-terminal region, including the conserved RXG motifs, was observed in addition to the polymorphs of the binding mode of the ligands. One of the RXG motifs covers the active site with an elongated random coil when the ligands are well-ordered. Conversely, the other RXG motif was located away from the active site with a helical structure. The heterogeneous C-terminal regions suggest alternating structural transitions of the RXG motifs that result in closed and open states of the active sites. Site-directed mutagenesis studies demonstrated that the conserved glycine residue cannot be replaced. We propose that the putative structural transitions of the order/disorder of N-terminal regions and the closed/open states of C-terminal regions may cooperate and be important for the catalytic mechanism of NDPS1. Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.,Imaizumi R, Matsuura H, Yanai T, Takeshita K, Misawa S, Yamaguchi H, Sakai N, Miyagi-Inoue Y, Suenaga-Hiromori M, Waki T, Kataoka K, Nakayama T, Yamamoto M, Takahashi S, Yamashita S Chembiochem. 2024 Apr 2;25(7):e202300796. doi: 10.1002/cbic.202300796. Epub 2024 , Jan 29. PMID:38225831[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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