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Structural basis of kinetic variations in Sucrose Phosphate Phosphatase (SPP) of rice and Anabaena unveiled through computational analysis

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Abstract

Sucrose is an important storage form of assimilated carbon in many plant species. Unlike other sucrose biosynthetic enzymes, Sucrose Phosphate Phosphatase (SPP), the terminal enzyme in sucrose biosynthetic pathway, is the least understood. SPPs from different organisms have different kinetic properties. The current study focuses on the structural differences among SPP homologues and unveils the probable structural basis of kinetic variations. We have employed computational methods of molecular modeling and structure comparisons and identified structural variations in some of the substrate binding residues, amino acid substitutions in regions that are lining the active site and minute structural differences that can enhance the nucleophilicity of a catalytic nucleophile (Asp 9 ). We report a structurally and hence functionally important amino acid substitution (Asp 159 by Alanine) in one of the rice SPP isoforms, which can result in the disruption of a H-bond that helps in binding of sucrose at the active site of the enzyme. In this paper we discuss the structural basis of enhanced catalytic efficiency of rice SPP in comparison with a cyanobacterium (Anabaena variabilis). The natural mutations identified in our analysis of the SPP catalytic domain would be useful in re-designing the enzyme for enhanced catalytic efficiency and higher sucrose production.

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Abbreviations

SPP:

Sucrose phosphate Phosphatase

SPS:

Sucrose phosphate Synthase

HAD:

Halo Acid Dehydrogenase

PSI-BLAST:

Position Specific Iterative BLAST

GDT:

Global Distance Test

MSA:

Multiple Sequence Alignment

LGA:

Local Global Alignment

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Acknowledgments

Authors thank Sugarcane Breeding Institute, Coimbatore for infrastructure facilities. DPS and NS are supported by Indian Council of Agricultural Research.

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Authors and Affiliations

  1. Sugarcane Breeding Institute, ICAR, Coimbatore, India

    Divya P. Syamaladevi, Neethi Jayaraman & N. Subramonian

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  1. Divya P. Syamaladevi
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  2. Neethi Jayaraman
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  3. N. Subramonian
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Correspondence to Divya P. Syamaladevi.

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Syamaladevi, D.P., Jayaraman, N. & Subramonian, N. Structural basis of kinetic variations in Sucrose Phosphate Phosphatase (SPP) of rice and Anabaena unveiled through computational analysis. J. Plant Biochem. Biotechnol. 23, 358–365 (2014). https://doi.org/10.1007/s13562-013-0219-5

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  • DOI: https://doi.org/10.1007/s13562-013-0219-5

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