1FSI

CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA

Summary for 1FSI

• Entry DOI: 10.2210/pdb1fsi/pdb
• Descriptor: CYCLIC PHOSPHODIESTERASE, SULFATE ION (3 entities in total)
• Functional Keywords: adp-ribose 1'', 2''-cyclic phosphate, appr>p, 2', 3'-cyclic nucleotide phosphodiesterase, hydrolase
• Biological source: Arabidopsis thaliana (thale cress)
• Cellular location: Cytoplasm: O04147
• Total number of polymer chains: 3
• Total formula weight: 65395.37

Authors

Hofmann, A.,Zdanov, A.,Genschik, P.,Filipowicz, W.,Ruvinov, S.,Wlodawer, A. (deposition date: 2000-09-10, release date: 2000-11-22, Last modification date: 2024-11-20)

Primary citation

Hofmann, A.,Zdanov, A.,Genschik, P.,Ruvinov, S.,Filipowicz, W.,Wlodawer, A.
Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction.
EMBO J., 19:6207-6217, 2000

PubMed 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 A 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 alphabeta modules. Each lobe consists of two alpha-helices on the outer side of the molecule, framing a three- or four-stranded antiparallel beta-sheet in the core of the protein. The active site is formed at the interface of the two beta-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.

PubMed: 11080166
DOI: 10.1093/emboj/19.22.6207

Experimental method

X-RAY DIFFRACTION (2.5 Å)