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Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family.

Myllykoski M, Raasakka A, Lehtimäki M, Han H, Kursula I, Kursula P
J Mol Biol 425 4307-22 (2013)
Related entries: 2yoz, 2yp0, 2ypc, 2ype, 2yq9, 3zbr, 3zbs, 3zbz

Cited: 17 times
EuropePMC logo PMID: 23831225

Abstract

2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5-α7 loop is observed. The role of the N terminus of helix α7--unique for CNPase in the 2H family--during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating that the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.

Articles - 2yph mentioned but not cited (1)

  1. Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family. Myllykoski M, Raasakka A, Lehtimäki M, Han H, Kursula I, Kursula P. J Mol Biol 425 4307-4322 (2013)


Reviews citing this publication (5)

  1. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Shigematsu M, Kawamura T, Kirino Y. Front Genet 9 562 (2018)
  2. The myelin membrane-associated enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase: on a highway to structure and function. Raasakka A, Kursula P. Neurosci Bull 30 956-966 (2014)
  3. Structural and functional evolution of 2',3'-cyclic nucleotide 3'-phosphodiesterase. Myllykoski M, Seidel L, Muruganandam G, Raasakka A, Torda AE, Kursula P. Brain Res 1641 64-78 (2016)
  4. Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease. Raasakka A, Kursula P. Cells 9 E470 (2020)
  5. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. Huynh TN, Parker R. J Biol Chem 299 105139 (2023)

Articles citing this publication (11)

  1. Antagonistic Functions of MBP and CNP Establish Cytosolic Channels in CNS Myelin. Snaidero N, Velte C, Myllykoski M, Raasakka A, Ignatev A, Werner HB, Erwig MS, Möbius W, Kursula P, Nave KA, Simons M. Cell Rep 18 314-323 (2017)
  2. Structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral RNase L antagonist. Ogden KM, Hu L, Jha BK, Sankaran B, Weiss SR, Silverman RH, Patton JT, Prasad BV. J Virol 89 6633-6645 (2015)
  3. Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase. Raasakka A, Myllykoski M, Laulumaa S, Lehtimäki M, Härtlein M, Moulin M, Kursula I, Kursula P. Sci Rep 5 16520 (2015)
  4. Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase. Remus BS, Jacewicz A, Shuman S. RNA 20 1697-1705 (2014)
  5. Identification of phosphorylated form of 2', 3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) as 46 kDa phosphoprotein in brain non-synaptic mitochondria overloaded by calcium. Azarashvili T, Krestinina O, Galvita A, Grachev D, Baburina Y, Stricker R, Reiser G. J Bioenerg Biomembr 46 135-145 (2014)
  6. Malonate in the nucleotide-binding site traps human AKAP18γ/δ in a novel conformational state. Bjerregaard-Andersen K, Østensen E, Scott JD, Taskén K, Morth JP. Acta Crystallogr F Struct Biol Commun 72 591-597 (2016)
  7. Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase. Myllykoski M, Kursula P. PLoS One 12 e0170355 (2017)
  8. Crystal structure of the RNA 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans. Han W, Cheng J, Zhou C, Hua Y, Zhao Y. Acta Crystallogr F Struct Biol Commun 73 276-280 (2017)
  9. Protein target highlights in CASP15: Analysis of models by structure providers. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Proteins 91 1571-1599 (2023)
  10. Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1. Nomura Y, Montemayor EJ, Virta JM, Hayes SM, Butcher SE. Nucleic Acids Res 48 1423-1434 (2020)
  11. Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase. Muruganandam G, Raasakka A, Myllykoski M, Kursula I, Kursula P. BMC Biochem 18 7 (2017)


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