PDBsum entry 4kg4

Hydrolase

PDB id: 4kg4

Contents

Protein chains

138 a.a.

141 a.a.

Waters ×128

PDB id:

4kg4

Name:

Hydrolase

Title:

Crystal structure of saccharomyces cerevisiae dcp2 nudix domain (e198q mutation)

Structure:

mRNA-decapping enzyme subunit 2. Chain: a, b. Fragment: catalytic nudix domain. Synonym: protein psu1. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: dcp2, n1917, psu1, ynl118c. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.189 R-free: 0.214

Authors:

R.A.Aglietti,S.N.Floor,J.D.Gross

Key ref:

R.A.Aglietti et al. (2013). Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2. Structure, 21, 1571-1580. PubMed id: 23911090 DOI: 10.1016/j.str.2013.06.021

Date:

28-Apr-13 Release date: 21-Aug-13

Protein chain

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

Seq: 970 a.a.

Struc: 138 a.a.*

Protein chain

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

Seq: 970 a.a.

Struc: 141 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: 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.str.2013.06.021

Structure 21:1571-1580 (2013)

PubMed id: 23911090

Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2.

R.A.Aglietti, S.N.Floor, C.L.McClendon, M.P.Jacobson, J.D.Gross.

ABSTRACT

Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.