PDBsum entry 2nug

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/RNA PDB id
Protein chains
216 a.a. *
_MG ×19
Waters ×445
* Residue conservation analysis
PDB id:
Name: Hydrolase/RNA
Title: Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 1.7-angstrom resolution
Structure: 5'-r(p Ap Ap Gp Gp Up Cp Ap Up Up Cp G)-3'. Chain: c, d. Engineered: yes. 5'-r(p Ap Gp Up Gp Gp Cp Cp Up Up Gp C)-3'. Chain: e, f. Engineered: yes. Ribonuclease iii. Chain: a, b. Synonym: rnase iii.
Source: Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.70Å     R-factor:   0.194     R-free:   0.220
Authors: J.H.Gan,G.Shaw,J.E.Tropea,D.S.Waugh,D.L.Court,X.Ji
Key ref: J.Gan et al. (2008). A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol, 67, 143-154. PubMed id: 18047582 DOI: 10.1111/j.1365-2958.2007.06032.x
09-Nov-06     Release date:   20-Nov-07    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 216 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Ribonuclease Iii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   8 terms 
  Biochemical function     hydrolase activity     6 terms  


DOI no: 10.1111/j.1365-2958.2007.06032.x Mol Microbiol 67:143-154 (2008)
PubMed id: 18047582  
A stepwise model for double-stranded RNA processing by ribonuclease III.
J.Gan, G.Shaw, J.E.Tropea, D.S.Waugh, D.L.Court, X.Ji.
RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21133991 K.Kim, S.H.Sim, C.O.Jeon, Y.Lee, and K.Lee (2011).
Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III.
  FEMS Microbiol Lett, 315, 30-37.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21138964 Z.Shi, R.H.Nicholson, R.Jaggi, and A.W.Nicholson (2011).
Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates.
  Nucleic Acids Res, 39, 2756-2768.  
20814424 P.Braglia, K.Heindl, A.Schleiffer, J.Martinez, and N.J.Proudfoot (2010).
Role of the RNA/DNA kinase Grc3 in transcription termination by RNA polymerase I.
  EMBO Rep, 11, 758-764.  
20946981 R.Stefl, F.C.Oberstrass, J.L.Hood, M.Jourdan, M.Zimmermann, L.Skrisovska, C.Maris, L.Peng, C.Hofr, R.B.Emeson, and F.H.Allain (2010).
The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific readout of the minor groove.
  Cell, 143, 225-237.
PDB codes: 2l2j 2l2k 2l3c 2l3j
18927112 H.S.Soifer, M.Sano, K.Sakurai, P.Chomchan, P.Saetrom, M.A.Sherman, M.A.Collingwood, M.A.Behlke, and J.J.Rossi (2008).
A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs.
  Nucleic Acids Res, 36, 6511-6522.  
18641914 K.Zenke, and K.H.Kim (2008).
Functional characterization of the RNase III gene of rock bream iridovirus.
  Arch Virol, 153, 1651-1656.  
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.