PDBsum entry 3i61

Hydrolase/RNA

PDB id: 3i61

Contents

Protein chain

509 a.a. *

DNA/RNA

Ligands

ADP-BEF

Metals

_MG

Waters ×218

* Residue conservation analysis

PDB id:

3i61

Name:

Hydrolase/RNA

Title:

Structure of mss116p bound to ssrna and adp-beryllium fluoride

Structure:

Atp-dependent RNA helicase mss116. Chain: a. Fragment: unp residues 37 to 597. Engineered: yes. 5'-r( Up Up Up Up Up Up Up Up Up U)-3'. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: mss116, yd9346.05c, ydr194c. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: RNA fragment commercially available

Resolution:

2.10Å R-factor: 0.188 R-free: 0.221

Authors:

M.Del Campo,A.M.Lambowitz

Key ref:

M.Del Campo and A.M.Lambowitz (2009). Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA. Mol Cell, 35, 598-609. PubMed id: 19748356

Date:

06-Jul-09 Release date: 08-Sep-09

Protein chain

P15424  (MS116_YEAST) -  ATP-dependent RNA helicase MSS116, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 664 a.a.

Struc: 509 a.a.

DNA/RNA chain

U-U-U-U-U-U-U-U-U-U 10 bases

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

Mol Cell 35:598-609 (2009)

PubMed id: 19748356

Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.

M.Del Campo, A.M.Lambowitz.

ABSTRACT

The yeast DEAD box protein Mss116p is a general RNA chaperone that functions in mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Here we determined high-resolution X-ray crystal structures of Mss116p complexed with an RNA oligonucleotide and ATP analogs AMP-PNP, ADP-BeF(3)(-), or ADP-AlF(4)(-). The structures show the entire helicase core acting together with a functionally important C-terminal extension. In all structures, the helicase core is in a closed conformation with a wedge alpha helix bending RNA 3' of the central bound nucleotides, as in previous DEAD box protein structures. Notably, Mss116p's C-terminal extension also bends RNA 5' of the central nucleotides, resulting in RNA crimping. Despite reported functional differences, we observe few structural changes in ternary complexes with different ATP analogs. The structures constrain models of DEAD box protein function and reveal a strand separation mechanism in which a protein uses two wedges to act as a molecular crimper.