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Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium

Authors

  • Hongyan Zheng,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Alina Beliavsky,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Anatoli Tchigvintsev,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Joseph S. Brunzelle,

    1. Department of Molecular Pharmacology and Biological Chemistry, Center for Structural Genomics of Infectious Diseases, Midwest Center for Structural Genomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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  • Greg Brown,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Robert Flick,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Elena Evdokimova,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    2. Department of Molecular Pharmacology and Biological Chemistry, Center for Structural Genomics of Infectious Diseases, Midwest Center for Structural Genomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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  • Zdzislaw Wawrzak,

    1. Department of Molecular Pharmacology and Biological Chemistry, Center for Structural Genomics of Infectious Diseases, Midwest Center for Structural Genomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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  • Radhakrishnan Mahadevan,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Wayne F. Anderson,

    1. Department of Molecular Pharmacology and Biological Chemistry, Center for Structural Genomics of Infectious Diseases, Midwest Center for Structural Genomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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  • Alexei Savchenko,

    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    2. Department of Molecular Pharmacology and Biological Chemistry, Center for Structural Genomics of Infectious Diseases, Midwest Center for Structural Genomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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  • Alexander F. Yakunin

    Corresponding author
    1. Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    • Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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  • Coordinates and structure factors have been deposited under accession codes 3ETF (apo-structure) and 3EFV (NAD+ complex).

Abstract

Aldehyde dehydrogenases are found in all organisms and play an important role in the metabolic conversion and detoxification of endogenous and exogenous aldehydes. Genomes of many organisms including Escherichia coli and Salmonella typhimurium encode two succinate semialdehyde dehydrogenases with low sequence similarity and different cofactor preference (YneI and GabD). Here, we present the crystal structure and biochemical characterization of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from S. typhimurium. This enzyme shows high activity and affinity toward succinate semialdehyde and exhibits substrate inhibition at concentrations of SSA higher than 0.1 mM. YneI can use both NAD+ and NADP+ as cofactors, although affinity to NAD+ is 10 times higher. High resolution crystal structures of YneI were solved in a free state (1.85 Å) and in complex with NAD+ (1.90 Å) revealing a two domain protein with the active site located in the interdomain interface. The NAD+ molecule is bound in the long channel with its nicotinamide ring positioned close to the side chain of the catalytic Cys268. Site-directed mutagenesis demonstrated that this residue, as well as the conserved Trp136, Glu365, and Asp426 are important for activity of YneI, and that the conserved Lys160 contributes to the enzyme preference to NAD+. Our work has provided further insight into the molecular mechanisms of substrate selectivity and activity of succinate semialdehyde dehydrogenases. © 2012 Wiley Periodicals, Inc.

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