PDBsum entry 2a6t

RNA binding protein,hydrolase

PDB id: 2a6t

Contents

Protein chains

230 a.a. *

173 a.a. *

Waters ×107

* Residue conservation analysis

PDB id:

2a6t

Name:

RNA binding protein,hydrolase

Title:

Crystal structure of s.Pombe mRNA decapping enzyme dcp2p

Structure:

Spac19a8.12. Chain: a, b. Fragment: n-terminal conserved region. Synonym: mRNA decapping enzyme dcp2. Engineered: yes

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.250 R-free: 0.289

Authors:

M.She,N.Chen,H.Song

Key ref:

M.She et al. (2006). Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe. Nat Struct Mol Biol, 13, 63-70. PubMed id: 16341225 DOI: 10.1038/nsmb1033

Date:

04-Jul-05 Release date: 20-Dec-05

Protein chain

O13828  (DCP2_SCHPO) -  mRNA decapping complex subunit 2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 741 a.a.

Struc: 230 a.a.

Protein chain

O13828  (DCP2_SCHPO) -  mRNA decapping complex subunit 2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Seq: 741 a.a.

Struc: 173 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.-.-.-

DOI no: 10.1038/nsmb1033

Nat Struct Mol Biol 13:63-70 (2006)

PubMed id: 16341225

Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe.

M.She, C.J.Decker, N.Chen, S.Tumati, R.Parker, H.Song.

ABSTRACT

Decapping is a key step in both general and nonsense-mediated 5' --> 3' mRNA-decay pathways. Removal of the cap structure is catalyzed by the Dcp1-Dcp2 complex. The crystal structure of a C-terminally truncated Schizosaccharomyces pombe Dcp2p reveals two distinct domains: an all-helical N-terminal domain and a C-terminal domain that is a classic Nudix fold. The C-terminal domain of both Saccharomyces cerevisiae and S. pombe Dcp2p proteins is sufficient for decapping activity, although the N-terminal domain can affect the efficiency of Dcp2p function. The binding of Dcp2p to Dcp1p is mediated by a conserved surface on its N-terminal domain, and the N-terminal domain is required for Dcp1p to stimulate Dcp2p activity. The flexible nature of the N-terminal domain relative to the C-terminal domain suggests that Dcp1p binding to Dcp2p may regulate Dcp2p activity through conformational changes of the two domains.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of spDcp2n and comparison with other Nudix enzymes. (a) Schematic representation of the domain organization of Dcp2p from S. pombe. (b) Ribbon diagram of spDcp2n. Orange, the N-terminal helical domain; light green, the C-terminal Nudix domain; red, the Nudix motif. Secondary structure elements are labeled. (c) Structure of Ap4AP in complex with a phosphate and AMP (PDB entry 1KTG). Sticks, AMP and phosphates; purple, the Nudix motif. (d) Structure of ADPRP in complex with ADP-ribose (PDB entry 1G9Q). Green, subunit A; gray, subunit B; sticks, ADP-ribose; magenta, the Nudix motif. The view of the Nudix domain for subunit A is the same as those for spDcp2n and Ap4AP.

Figure 3.
Figure 3. Surface views of spDcp2n. (a) Surface representation of spDcp2n showing the regions of high to low sequence conservation among the eukaryotic Dcp2 proteins. Besides the highly conserved Nudix motif, a large conserved patch in the N-terminal domain is revealed and corresponding residues are labeled. (b) Back view of the molecular surface of spDcp2n showing the sequence conservation. The molecule is rotated 180° along a vertical axis relative to the view in a.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 63-70) copyright 2006.

Figures were selected by an automated process.