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PDBsum entry 3i5x

Go to PDB code: 
protein dna_rna ligands metals links
Hydrolase/RNA PDB id
3i5x
Jmol
Contents
Protein chain
509 a.a. *
DNA/RNA
Ligands
ANP
Metals
_MG
Waters ×289
* Residue conservation analysis
PDB id:
3i5x
Name: Hydrolase/RNA
Title: Structure of mss116p bound to ssrna and amp-pnp
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:
1.90Å     R-factor:   0.192     R-free:   0.225
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15424  (MS116_YEAST) -  ATP-dependent RNA helicase MSS116, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
664 a.a.
509 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     3 terms  

 

 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22940866 A.L.Mallam, M.Del Campo, B.Gilman, D.J.Sidote, and A.M.Lambowitz (2012).
Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p.
  Nature, 490, 121-125.
PDB codes: 4db2 4db4
20813532 E.Jankowsky (2011).
RNA helicases at work: binding and rearranging.
  Trends Biochem Sci, 36, 19-29.  
20307546 A.L.Bifano, E.M.Turk, and M.G.Caprara (2010).
Structure-guided mutational analysis of a yeast DEAD-box protein involved in mitochondrial RNA splicing.
  J Mol Biol, 398, 429-443.  
20472641 S.Lattmann, B.Giri, J.P.Vaughn, S.A.Akman, and Y.Nagamine (2010).
Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU.
  Nucleic Acids Res, 38, 6219-6233.  
19747077 M.Hilbert, A.R.Karow, and D.Klostermeier (2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.
  Biol Chem, 390, 1237-1250.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.