PDBsum entry 4px9

Translation, RNA binding protein

PDB id: 4px9

Contents

Protein chains

262 a.a.

Ligands

ADP ×3

PDB id:

4px9

Name:

Translation, RNA binding protein

Title:

Dead-box RNA helicase ddx3x domain 1 with n-terminal atp-binding loop

Structure:

Atp-dependent RNA helicase ddx3x. Chain: a, b, c. Fragment: unp residues 135-407. Synonym: dead box protein 3, x-chromosomal, dead box, x isoform, helicase-like protein 2, hlp2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dbx, ddx3, ddx3x. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.31Å R-factor: 0.255 R-free: 0.285

Authors:

L.B.Epling,C.R.Grace,B.R.Lowe,J.F.Partridge,E.J.Enemark

Key ref:

L.B.Epling et al. (2015). Cancer-associated mutants of RNA helicase DDX3X are defective in RNA-stimulated ATP hydrolysis. J Mol Biol, 427, 1779-1796. PubMed id: 25724843 DOI: 10.1016/j.jmb.2015.02.015

Date:

22-Mar-14 Release date: 11-Mar-15

Protein chains

O00571  (DDX3X_HUMAN) -  ATP-dependent RNA helicase DDX3X from Homo sapiens

Seq: 662 a.a.

Struc: 262 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2015.02.015

J Mol Biol 427:1779-1796 (2015)

PubMed id: 25724843

Cancer-associated mutants of RNA helicase DDX3X are defective in RNA-stimulated ATP hydrolysis.

L.B.Epling, C.R.Grace, B.R.Lowe, J.F.Partridge, E.J.Enemark.

ABSTRACT

The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension ("ATP-binding loop", ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specifically with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. Taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.