1JH7

Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana

Summary for 1JH7

• Entry DOI: 10.2210/pdb1jh7/pdb
• Related: 1fsi 1jh6
• Descriptor: cyclic phosphodiesterase, SULFATE ION, URIDINE-2',3'-VANADATE, ... (4 entities in total)
• Functional Keywords: adp-ribose 1'', 2''-cyclic phosphate, rna processing, 2', 3'-cyclic nucleotide phosphodiesterase, 3'-cyclic uridine vanadate, hydrolase
• Biological source: Arabidopsis thaliana (thale cress)
• Cellular location: Cytoplasm: O04147
• Total number of polymer chains: 1
• Total formula weight: 22580.80

Authors

Hofmann, A.,Grella, M.,Botos, I.,Filipowicz, W.,Wlodawer, A. (deposition date: 2001-06-27, release date: 2002-02-06, Last modification date: 2024-10-16)

Primary citation

Hofmann, A.,Grella, M.,Botos, I.,Filipowicz, W.,Wlodawer, A.
Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana.
J.Biol.Chem., 277:1419-1425, 2002

PubMed Abstract: The crystal structure of the semireduced form of cyclic nucleotide phosphodiesterase (CPDase) from Arabidopsis thaliana has been solved by molecular replacement and refined at the resolution of 1.8 A. We have previously reported the crystal structure of the native form of this enzyme, whose main target is ADP-ribose 1",2"-cyclic phosphate, a product of the tRNA splicing reaction. CPDase possesses six cysteine residues, four of which are involved in forming two intra-molecular disulfide bridges. One of these bridges, between Cys-104 and Cys-110, is opened in the semireduced CPDase, whereas the other remains intact. This change of the redox state leads to a conformational rearrangement in the loop covering the active site of the protein. While the native structure shows this partially disordered loop in a coil conformation, in the semireduced enzyme the N-terminal lobe of this loop winds up and elongates the preceding alpha-helix. The semireduced state of CPDase also enabled co-crystallization with a putative inhibitor of its enzymatic activity, 2',3'-cyclic uridine vanadate. The ligand is bound within the active site, and the mode of binding is in agreement with the previously proposed enzymatic mechanism. Selected biophysical properties of the oxidized and the semireduced CPDase are also discussed.

PubMed: 11694509
DOI: 10.1074/jbc.M107889200

Experimental method

X-RAY DIFFRACTION (2.4 Å)