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Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus

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Abstract

Dihydrodipicolinate synthase (DHDPS, E.C.4.2.1.52) catalyzes the first committed step in the lysine biosynthetic pathway: the condensation of (S)-aspartate semialdehyde and pyruvate to form (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. Since (S)-lysine biosynthesis does not occur in animals, DHDPS is an attractive target for rational antibiotic and herbicide design. Here, we report the crystal structure of DHDPS from a hyperthermophilic bacterium Aquifex aeolicus (AqDHDPS). l-Lysine is used as an important animal feed additive where the production is at the level of 1.5 million tons per year. The biotechnological manufacture of lysine has been going for more than 50 years which includes over synthesis and reverse engineering of DHDPS. AqDHDPS revealed a unique disulfide linkage which is not conserved in the homologues of AqDHDPS. In silico mutation of C139A and intermolecular ion-pair residues and the subsequent molecular dynamics simulation of the mutants showed that these residues are critical for the stability of AqDHDPS tetramer. MD simulations of AqDHDPS at three different temperatures (303, 363 and 393 K) revealed that the molecule is stable at 363 K. Thus, this structural and in silico study of AqDHDPS likely provides additional details towards the rational and structure-based design of hyper-l-lysine producing bacterial strains.

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Acknowledgments

This work was supported by the RIKEN Structural Genomic/Proteomics Initiative (RSGI), the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science and Technology of Japan. US thanks the Department of Science and Technology (DST), Government of India for the financial support in the form of INSPIRE fellowship.

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Authors and Affiliations

  1. Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600 025, India

    Upasana Sridharan & Karthe Ponnuraj

  2. RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan

    Akio Ebihara, Seiki Kuramitsu & Thirumananseri Kumarevel

  3. Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan

    Seiki Kuramitsu

  4. Structural Biology Laboratory, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan

    Shigeyuki Yokoyama & Thirumananseri Kumarevel

  5. Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan

    Shigeyuki Yokoyama

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  1. Upasana Sridharan
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  2. Akio Ebihara
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  3. Seiki Kuramitsu
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  4. Shigeyuki Yokoyama
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  5. Thirumananseri Kumarevel
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  6. Karthe Ponnuraj
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Correspondence to Karthe Ponnuraj.

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Communicated by H. Atomi.

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Sridharan, U., Ebihara, A., Kuramitsu, S. et al. Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus . Extremophiles 18, 973–985 (2014). https://doi.org/10.1007/s00792-014-0667-4

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