Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus

Bobbili, Kishore Babu; Sivaji, N.; Priya, Badma; Suguna, K.; Surolia, Avadhesha

doi:10.1016/j.str.2023.02.008

Cited by 14 publications

(13 citation statements)

References 78 publications

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“…A comparison of the two subunits revealed a 1.12 Å root-mean-square deviation (RMSD) for the Cα atoms (Figure b). Each monomer of the heterodimer resembles that of the recently reported crystal structure of homodimeric PP2 Cus17 (PDB 7VWB) from Cucumis sativus , consisting of a β-hairpin and two antiparallel four-stranded twisted β-sheets (I and II) forming a β-sandwich fold (0.948 Å (HRSα vs Cus17) and 1.346 Å (HRSβ vs Cus17) RMSD for Cα-atoms) (Figure b) . Compared to Cus17, the HRS subunits have a longer N -terminus that forms two additional β strands, β1 and β2, with the latter serving as part of twisted β-sheet I (Figures b and Figure S4).…”

Section: Resultsmentioning

confidence: 99%

“…The bottom of the β barrel is closed by two β-sheets comprising β1(α)/β4(β)/β6(β) and β5(α)/β4(α)/β1(β) (Figure S5). In striking contrast to the HRS heterodimer, the homodimeric Cus17 has no cavity at the homodimer interface because of the topological difference in dimerization …”

Section: Resultsmentioning

confidence: 99%

“…On the one hand, the Cus17 monomer contacts the other monomer at the edges of the two β sheets I and II in a side-by-side manner, forming an extended eight-stranded β sheet (Figure S5). 21 The dimerization of Cus17 also involves a disulfide bond linkage between two Cys34 residues on the β hairpin loops of each monomer. 21 On the other hand, the HRS heterodimerization is facilitated by the multilateral association of β-strands (Figure S5).…”

Section: ■ Introductionmentioning

confidence: 99%

“…Each monomer of the heterodimer resembles that of the recently reported crystal structure of homodimeric PP2 Cus17 (PDB 7VWB) from Cucumis sativus, consisting of a β-hairpin and two antiparallel four-stranded twisted β-sheets (I and II) forming a β-sandwich fold (0.948 Å (HRSα vs Cus17) and 1.346 Å (HRSβ vs Cus17) RMSD for Cα-atoms) (Figure 2b). 21 Compared to Cus17, the HRS subunits have a longer N-terminus that forms two additional β strands, β1 and β2, with the latter serving as part of twisted β-sheet I (Figures 2b and Figure S4). Another notable difference is that the β6 strands in HRSα and HRSβ are shorter than that in Cus17, while the β5 strand was only found in HRSα.…”

Section: ■ Introductionmentioning

confidence: 99%

“…21 The dimerization of Cus17 also involves a disulfide bond linkage between two Cys34 residues on the β hairpin loops of each monomer. 21 On the other hand, the HRS heterodimerization is facilitated by the multilateral association of β-strands (Figure S5). The β sheets I of the two units face each other via interactions between β2(α)/β10(β) and β10(α)/β2(β) (Figure S5).…”

Section: ■ Introductionmentioning

confidence: 99%

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Structural and Mechanistic Insights into the C–C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase

Ushimaru,

Ding,

Mori

et al. 2023

J. Am. Chem. Soc.

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Hinokiresinol synthase (HRS) from Asparagus of f icinalis consists of two subunits, α and β, and catalyzes an unusual decarboxylative rearrangement reaction of 4-coumaryl 4-coumarate to generate (Z)hinokiresinol with complete stereoselectivity. Herein, we describe the mechanism of rearrangement catalysis and the role played by the heterodimeric HRS, through structural and computational analyses. Our results suggest that the HRS reaction is unlikely to proceed via the previously hypothesized Claisen rearrangement mechanism. Instead, we propose that the 4-coumaryl 4-coumarate substrate is first cleaved into coumarate and an extended p-quinone methide, which then recombine to generate a new C−C bond. These processes are facilitated by proton transfers mediated by the basic residues (α-Lys164, α-Arg169, β-Lys168, and β-Arg173) in the cavity at the heterodimer interface. The active site residues, α-Asp165, β-Asp169, β-Trp17, β-Met136, and β-Ala171, play crucial roles in controlling the regioselectivity of the coupling between the fragmented intermediates as well as the stereoselectivity of the decarboxylation step, leading to the formation of the (Z)-hinokiresinol product.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Structural and Mechanistic Insights into the C–C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase

Ushimaru,

Ding,

Mori

et al. 2023

J. Am. Chem. Soc.

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Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Ouabane,

Zaki,

Alaqarbeh

et al. 2024

ChemistrySelect

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Nitrobenzene derivatives present an environmental concern to aquatic organisms, as well as a potential adverse effects on human health due to their toxicity. Therefore, monitoring nitrobenzene contamination levels is critical to protect both the ecosystem and the public. This study aims to quantitatively correlate the toxicity of nitrobenzene derivatives to their chemical structures using computational chemistry methods such as 3D‐QSPR, HQSPR, Molecular Docking and MD simulation. Additionally, to investigate the type of interactions and stability of nitrobenzene derivatives with the PP2 protein involved in the Phloem protein 2 (PP2). From each computational method a prediction model was extracted HQSPR (Atomic, Bonds, Donor/Acceptor, 3D‐QSPR (Steric, Electrostatic, Hydrophobic, Acceptor), and used for the design of X1 and X2 new nitrobenzene derivatives, which showed remarkable stability and better interactions. This study contributes to the understanding of the nitrobenzene derivatives’ toxicity and offers materials towards the understanding of the mechanism of action of these substances in protein–ligand interactions.

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Structural and functional diversity of plant lectins

Osterne,

Van Damme

2024

Defense-Related Proteins in Plants

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Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus

Cited by 14 publications

References 78 publications

Structural and Mechanistic Insights into the C–C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase

Structural and Mechanistic Insights into the C–C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase

Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Structural and functional diversity of plant lectins

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