PDBsum entry 2jvb

Hydrolase

PDB id: 2jvb

Contents

Protein chain

146 a.a. *

* Residue conservation analysis

PDB id:

2jvb

Name:

Hydrolase

Title:

Solution structure of catalytic domain of ydcp2

Structure:

mRNA-decapping enzyme subunit 2. Chain: a. Synonym: protein psu1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dcp2, psu1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

10 models

Authors:

M.Deshmukh,J.Gross

Key ref:

M.V.Deshmukh et al. (2008). mRNA decapping is promoted by an RNA-binding channel in Dcp2. Mol Cell, 29, 324-336. PubMed id: 18280238 DOI: 10.1016/j.molcel.2007.11.027

Date:

16-Sep-07 Release date: 04-Mar-08

Protein chain

P53550  (DCP2_YEAST) -  m7GpppN-mRNA hydrolase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 970 a.a.

Struc: 146 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.62 - 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
• Reaction: a 5'-end (N₇-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = N(7)-methyl-GDP + a 5'-end phospho-ribonucleoside in mRNA + 2 H⁺

DOI no: 10.1016/j.molcel.2007.11.027

Mol Cell 29:324-336 (2008)

PubMed id: 18280238

mRNA decapping is promoted by an RNA-binding channel in Dcp2.

M.V.Deshmukh, B.N.Jones, D.U.Quang-Dang, J.Flinders, S.N.Floor, C.Kim, J.Jemielity, M.Kalek, E.Darzynkiewicz, J.D.Gross.

ABSTRACT

Cap hydrolysis by Dcp2 is a critical step in several eukaryotic mRNA decay pathways. Processing requires access to cap-proximal nucleotides and the coordinated assembly of a decapping mRNP, but the mechanism of substrate recognition and regulation by protein interactions have remained elusive. Using NMR spectroscopy and kinetic analyses, we show that yeast Dcp2 resolves interactions with the cap and RNA body using a bipartite surface that forms a channel intersecting the catalytic and regulatory Dcp1-binding domains. The interaction with cap is weak but specific and requires binding of the RNA body to a dynamic interface. The catalytic step is stimulated by Dcp1 and its interaction domain, likely through a substrate-induced conformational change. Thus, activation of the decapping mRNP is restricted by access to 5'-proximal nucleotides, a feature that could act as a checkpoint in mRNA metabolism.

Selected figure(s)

Figure 5.
Figure 5. The Dorsal Surface Fluctuates on the ms-μs Timescale
(A) Representative relaxation dispersion curves obtained on the Nudix domain of yDcp2 labeled with ^1H/^13C at methyl positions of Ile(δ[1]), Leu, and Val recorded at 600 MHz (blue) and 800 MHz (red) field strengths, respectively. The δ[1] methyl group of Box B residue Leu223 is severely broadened by ms-μs dynamics, while that of Ile147 within the Nudix box is less affected. Errors in R[2] were propagated using standard procedures with uncertainty in individual peak intensities derived from NMRPipe (Delaglio et al., 1995).
(B) Sequence alignment of a conserved region within the dorsal surface (Box B) from several species.
(C) Rates of dynamical interconversion between two states (k[ex]) encoded in sphere diameters mapped onto C[β] positions of Ile, Leu, and Val within the structure of the Nudix domain. Cyan spheres denote measurable ms-μs motions, while gray spheres indicate methyl groups that are not dynamic on ms-μs timescales.

Figure 6.
Figure 6. Model of RNA Binding by yDcp2
(Left) Residues lining the surface of the Nudix domain serve as the base of a channel that runs between the Dcp1-binding domain and the catalytic center. (Center) Chemical shift changes of 29 nt nonhydrolyzable capped RNA mapped onto a homology model of yDcp2. (Right) Proposed path of the RNA body based on NMR mapping and biochemical and genetic data.

The above figures are reprinted by permission from Cell Press: Mol Cell (2008, 29, 324-336) copyright 2008.

Figures were selected by an automated process.