2YDB

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with 2',3'-cyclic NADP

Summary for 2YDB

• Entry DOI: 10.2210/pdb2ydb/pdb
• Related: 2XMI 2Y1P 2Y3X 2YDC 2YDD
• Descriptor: 2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: hydrolase, myelin, nervous system
• Biological source: MUS MUSCULUS (HOUSE MOUSE)
• Cellular location: Membrane ; Lipid-anchor : P16330
• Total number of polymer chains: 1
• Total formula weight: 25037.33

Authors

Myllykoski, M.,Kursula, P. (deposition date: 2011-03-18, release date: 2012-03-21, Last modification date: 2023-12-20)

Primary citation

Myllykoski, M.,Raasakka, A.,Han, H.,Kursula, P.
Myelin 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase: Active- Site Ligand Binding and Molecular Conformation.
Plos One, 7:32336-, 2012

PubMed Abstract: The 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is a highly abundant membrane-associated enzyme in the myelin sheath of the vertebrate nervous system. CNPase is a member of the 2H phosphoesterase family and catalyzes the formation of 2'-nucleotide products from 2',3'-cyclic substrates; however, its physiological substrate and function remain unknown. It is likely that CNPase participates in RNA metabolism in the myelinating cell. We solved crystal structures of the phosphodiesterase domain of mouse CNPase, showing the binding mode of nucleotide ligands in the active site. The binding mode of the product 2'-AMP provides a detailed view of the reaction mechanism. Comparisons of CNPase crystal structures highlight flexible loops, which could play roles in substrate recognition; large differences in the active-site vicinity are observed when comparing more distant members of the 2H family. We also studied the full-length CNPase, showing its N-terminal domain is involved in RNA binding and dimerization. Our results provide a detailed picture of the CNPase active site during its catalytic cycle, and suggest a specific function for the previously uncharacterized N-terminal domain.

PubMed: 22393399
DOI: 10.1371/JOURNAL.PONE.0032336

Experimental method

X-RAY DIFFRACTION (2.15 Å)