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  • Structure and mechanism of activity of the cyclic phosphodiesterase o Appr>p, a product of the tRNA splicing reaction

    Author(s)
    Hofmann, A
    Zdanov, A
    Genschik, P
    Ruvinov, S
    Filipowicz, W
    Wlodawer, A
    Griffith University Author(s)
    Hofmann, Andreas
    Year published
    2000
    Metadata
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    Abstract
    The crystal structure of the cyclic phosphodiesterase (CPDase) from Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was determined at 2.5 Å resolution. CPDase hydrolyzes ADP‐ribose 1″,2″‐cyclic phosphate (Appr>p), a product of the tRNA splicing reaction, to the monoester ADP‐ribose 1″‐phosphate (Appr‐1″p). The 181 amino acid protein shows a novel, bilobal arrangement of two αβ modules. Each lobe consists of two α‐helices on the outer side of the molecule, framing a three‐ or four‐stranded antiparallel β‐sheet in the core of the protein. The active site is formed at the interface of the two β‐sheets ...
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    The crystal structure of the cyclic phosphodiesterase (CPDase) from Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was determined at 2.5 Å resolution. CPDase hydrolyzes ADP‐ribose 1″,2″‐cyclic phosphate (Appr>p), a product of the tRNA splicing reaction, to the monoester ADP‐ribose 1″‐phosphate (Appr‐1″p). The 181 amino acid protein shows a novel, bilobal arrangement of two αβ modules. Each lobe consists of two α‐helices on the outer side of the molecule, framing a three‐ or four‐stranded antiparallel β‐sheet in the core of the protein. The active site is formed at the interface of the two β‐sheets in a water‐filled cavity involving residues from two H‐X‐T/S‐X motifs. This previously noticed motif participates in coordination of a sulfate ion. A solvent‐exposed surface loop (residues 100–115) is very likely to play a flap‐like role, opening and closing the active site. Based on the crystal structure and on recent mutagenesis studies of a homologous CPDase from Saccharomyces cerevisiae, we propose an enzymatic mechanism that employs the nucleophilic attack of a water molecule activated by one of the active site histidines.
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    Journal Title
    EMBO journal
    Volume
    19
    DOI
    https://doi.org/10.1093/emboj/19.22.6207
    Subject
    Biological Sciences
    Information and Computing Sciences
    Medical and Health Sciences
    Publication URI
    http://hdl.handle.net/10072/67468
    Collection
    • Journal articles

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