PDBsum entry 4tyw

RNA binding protein/RNA

PDB id: 4tyw

Contents

Protein chain

508 a.a.

DNA/RNA

Ligands

BEF

ADP

Metals

_MG ×2

Waters ×115

PDB id:

4tyw

Name:

RNA binding protein/RNA

Title:

Dead-box helicase mss116 bound to ssrna and adp-bef

Structure:

Atp-dependent RNA helicase mss116, mitochondrial. Chain: a. Fragment: unp residues 88-595. Engineered: yes. RNA (5'-r(p Ap Ap Ap Ap Ap Ap A)-3'). Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: mss116, ydr194c, yd9346.05c. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 4932

Resolution:

2.20Å R-factor: 0.218 R-free: 0.254

Authors:

A.L.Mallam,D.J.Sidote,A.M.Lambowitz

Key ref:

A.L.Mallam et al. (2014). Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. Elife, 3, e04630. PubMed id: 25497230 DOI: 10.7554/eLife.04630

Date:

09-Jul-14 Release date: 31-Dec-14

Protein chain

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

Seq: 664 a.a.

Struc: 508 a.a.

DNA/RNA chain

A-A-A-A-A-A-A 7 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

DOI no: 10.7554/eLife.04630

Elife 3:e04630 (2014)

PubMed id: 25497230

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.

A.L.Mallam, D.J.Sidote, A.M.Lambowitz.

ABSTRACT

How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.