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PDB:2A6T

Protein Name

mRNA decapping enzyme Dcp2p

Species

Schizosaccharomyces pombe

Biological Context

Messenger RNA(mRNA) is the transcript of DNA and works as a message (code) for protein translation. Posttranslational 5’ terminal capping and decapping are important for controlling mRNA expression level because the capped mRNA is stable and tolerant to degradation while the decapped mRNA liable to degradation. The protein described here, Dcp2p, is a component of the RNA decapping enzyme complex. Dcp2p contains the active site of the enzyme and requires non-catalytic Dcp1p to work as a holoenzyme. The active site of Dcp2p is named “Nudix domain”. Nudix domain is the conserved motif in the Nudix hydrolase family that catalyzes the hydrolysis of nucleotide phosphates.

Structure Description

2a6t2a6t_x2a6t_y

Shown here is the N terminal 266 residues of Schizosaccharomyces pombe Dcp2p. The N terminal ~300 residues of Dcp2 proteins are well conserved across different organisms and are essential for the decapping reaction. The Dcp2p contains all α-helical N terminal domain and α and β structure containing Nudix domain (fig1). The N terminal domain is the binding site of Dcp1p. Nudix domain is the catalytic domain. As in the other Nudix hydrolase, the active center “Nudix motif” is located in a loop-helix-loop structure(fig1 red). The consensus sequence of the Nudix motif is GX5EX7REUXEEXGU, in which X is any residue and U is Ile, Leu or Val. The activity of Nudix motif requires some divalent cations (magnesium and manganese) that bind to the glutamate residues. In particular, glutamate residues at position 16, 19 and 20 within the Nudix motif(Glu143, Glu146 and Glu147) and Glu192 at the C terminal of Nudix domain are considered to play an important role in catalysis(fig2).

fig1

fig1. N terminal 266 residues of Dcp2p. N teminal domain, Nudix domain and Nudix motif are colored as orange, green and red respectively.

fig2

fig2. Nudix motif of Dcp2p. Important glutamate residues for divalent cation binding are shown.

Protein Data Bank (PDB)

References

Source

She, M. Decker, C.J. Chen, N. Tumati, S. Parker, R. Song, H.; "Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe"; Nat.Struct.Mol.Biol.; (2006) 13:63-70 PubMed:16341225.

Others

author: Daisuke Ino


Japanese version:PDB:2A6T