8X37

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP

Summary for 8X37

• Entry DOI: 10.2210/pdb8x37/pdb
• Descriptor: Neryl-diphosphate synthase 1, DIMETHYLALLYL S-THIOLODIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: cis-prenyltransferase, transferase
• Biological source: Solanum lycopersicum (tomato)
• Total number of polymer chains: 2
• Total formula weight: 61416.21

Authors

Imaizumi, R.,Matsuura, H.,Yanai, T.,Takeshita, K.,Misawa, S.,Yamaguchi, H.,Sakai, N.,Miyagi-Inoue, Y.,Suenaga-Hiromori, M.,Kataoka, K.,Nakayama, T.,Yamamoto, M.,Takahashi, S.,Yamashita, S. (deposition date: 2023-11-12, release date: 2024-02-07, Last modification date: 2024-04-24)

Primary citation

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.
Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25:e202300796-e202300796, 2024

PubMed Abstract: Neryl diphosphate (C) 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.

PubMed: 38225831
DOI: 10.1002/cbic.202300796

Experimental method

X-RAY DIFFRACTION (1.98 Å)