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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 2024; 25:e202300796. [PMID: 38225831 DOI: 10.1002/cbic.202300796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Neryl diphosphate (C10) 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.
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Affiliation(s)
- Riki Imaizumi
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Hiroaki Matsuura
- RIKEN, SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Taro Yanai
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Kohei Takeshita
- RIKEN, SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Shuto Misawa
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | | | - Naoki Sakai
- RIKEN, SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | | | | | - Toshiyuki Waki
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Kunishige Kataoka
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Masaki Yamamoto
- RIKEN, SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Yamashita
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
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Kuroiwa F, Nishino A, Mandal Y, Honzawa M, Suenaga-Hiromori M, Suzuki K, Takani Y, Miyagi-Inoue Y, Yamaguchi H, Yamashita S, Takahashi S, Tozawa Y. Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule. Sci Rep 2022; 12:3734. [PMID: 35260628 PMCID: PMC8904820 DOI: 10.1038/s41598-022-07564-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Natural rubber of the Para rubber tree (Hevea brasiliensis) is synthesized as a result of prenyltransferase activity. The proteins HRT1, HRT2, and HRBP have been identified as candidate components of the rubber biosynthetic machinery. To clarify the contribution of these proteins to prenyltransferase activity, we established a cell-free translation system for nanodisc-based protein reconstitution and measured the enzyme activity of the protein-nanodisc complexes. Co-expression of HRT1 and HRBP in the presence of nanodiscs yielded marked polyisoprene synthesis activity. By contrast, neither HRT1, HRT2, or HRBP alone nor a complex of HRT2 and HRBP manifested such activity. Similar analysis of guayule (Parthenium argentatum) proteins revealed that three HRT1 homologs (PaCPT1-3) manifested prenyltransferase activity only when co-expressed with PaCBP, the homolog of HRBP. Our results thus indicate that two heterologous subunits form the core prenyltransferase of the rubber biosynthetic machinery. A recently developed structure modeling program predicted the structure of such heterodimer complexes including HRT1/HRBP and PaCPT2/PaCBP. HRT and PaCPT proteins were also found to possess affinity for a lipid membrane in the absence of HRBP or PaCBP, and structure modeling implicated an amphipathic α-helical domain of HRT1 and PaCPT2 in membrane binding of these proteins.
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Affiliation(s)
- Fu Kuroiwa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Akira Nishino
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Yasuko Mandal
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Masataka Honzawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | | | - Kakeru Suzuki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Yukie Takani
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | | | | | - Satoshi Yamashita
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
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