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In silico identification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from Phytophthora sojae

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Abstract

As part of an effort to obtain a fungal 1-aminocyclopropane-1-carboxylate deaminase encoding gene from Phytophthora sojae expressed sequence Tag database, we identify and characterize the ACCD from P. sojae using bioinformatics data mining tools and techniques. Computed structural model of P. sojae ACCD was found to consist of mixed α/β motifs and probable loops. The predicted model resembles the structure of Pseudomonas ACCD (RMSD-0.44 Å). The main differences observed between them are the presence of partial length of domain one, and longer helix α4. Ramachandran plot analysis revealed that portion of all residues falling into the most favorable regions was 95.0%. The substrate – and geometrical- docking of developed structure postulated functional capability of ACCD to carry out ACC cleavage reaction. The catalytic site in homo-tetrameric structure open to opposite directions separated by ∼37.97 Å distance arranged around central axis. This study provides a comprehensive identification and characterization of the ACCD in P. sojae and it may be helpful in the transcriptional and expression based study of P. sojae pathogenesis.

1-aminocyclopropane-1-carboxylate deaminase from Phytophthorasoja.

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Acknowledgments

The authors are grateful to Indian Council of Agricultural Research for Senior Research Fellowship to NS and Research Associateship to SK under the network project “Application of Microorganisms in Agricultural and Allied Sectors”. Infrastructure facility, support and encouragements by Director of the National Bureau of Agriculturally Important Microorganisms are duly acknowledged.

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  1. National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Mau Nath Bhanjan, 275101, Uttar Pradesh, India

    Nidhi Singh & Sudhanshu Kashyap

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  1. Nidhi Singh
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  2. Sudhanshu Kashyap
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Correspondence to Sudhanshu Kashyap.

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Singh, N., Kashyap, S. In silico identification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from Phytophthora sojae . J Mol Model 18, 4101–4111 (2012). https://doi.org/10.1007/s00894-012-1389-0

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