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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/RNA PDB id
2ez6
Jmol
Contents
Protein chains
218 a.a. *
DNA/RNA
Metals
_MG ×2
Waters ×298
* Residue conservation analysis
PDB id:
2ez6
Name: Hydrolase/RNA
Title: Crystal structure of aquifex aeolicus rnase iii (d44n) complexed with product of double-stranded RNA processing
Structure: 28-mer. Chain: c, d. Engineered: yes. Ribonuclease iii. Chain: a, b. Synonym: rnase iii. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.05Å     R-factor:   0.205     R-free:   0.258
Authors: J.Gan,J.E.Tropea,B.P.Austin,D.L.Court,D.S.Waugh,X.Ji
Key ref:
J.Gan et al. (2006). Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell, 124, 355-366. PubMed id: 16439209 DOI: 10.1016/j.cell.2005.11.034
Date:
10-Nov-05     Release date:   07-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67082  (RNC_AQUAE) -  Ribonuclease 3
Seq:
Struc: 		221 a.a.
218 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.26.3  - Ribonuclease Iii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     RNA processing   2 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1016/j.cell.2005.11.034 Cell 124:355-366 (2006)
PubMed id: 16439209  
 
 
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.
J.Gan, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, X.Ji.
 
  ABSTRACT  
 
Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by a signature motif in their active centers and a two-base 3' overhang in their products. While Dicer, which produces small interfering RNAs, is currently the focus of intense interest, the structurally simpler bacterial RNase III serves as a paradigm for the entire family. Here, we present the crystal structure of an RNase III-product complex, the first catalytic complex observed for the family. A 7 residue linker within the protein facilitates induced fit in protein-RNA recognition. A pattern of protein-RNA interactions, defined by four RNA binding motifs in RNase III and three protein-interacting boxes in dsRNA, is responsible for substrate specificity, while conserved amino acid residues and divalent cations are responsible for scissile-bond cleavage. The structure reveals a wealth of information about the mechanism of RNA hydrolysis that can be extrapolated to other RNase III family members.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The Flexible Linker and Induced Fit during dsRNA Binding 		Figure 5.
Figure 5. Schematic Representation of RNase III-dsRNA Interactions
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 124, 355-366) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20971974 B.Kolaczkowski, D.N.Hupalo, and A.D.Kern (2011).
Recurrent adaptation in RNA interference genes across the Drosophila phylogeny.
  Mol Biol Evol, 28, 1033-1042.  
21419681 E.S.Cenik, R.Fukunaga, G.Lu, R.Dutcher, Y.Wang, T.M.Tanaka Hall, and P.D.Zamore (2011).
Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease.
  Mol Cell, 42, 172-184.  
20739353 J.Starega-Roslan, J.Krol, E.Koscianska, P.Kozlowski, W.J.Szlachcic, K.Sobczak, and W.J.Krzyzosiak (2011).
Structural basis of microRNA length variety.
  Nucleic Acids Res, 39, 257-268.  
20846955 M.Brameier, A.Herwig, R.Reinhardt, L.Walter, and J.Gruber (2011).
Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs.
  Nucleic Acids Res, 39, 675-686.  
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.  
  20226070 G.A.Mueller, M.T.Miller, E.F.Derose, M.Ghosh, R.E.London, and T.M.Hall (2010).
Solution structure of the Drosha double-stranded RNA-binding domain.
  Silence, 1, 2.  
20071573 M.Hussain, A.M.Abraham, and S.Asgari (2010).
An Ascovirus-encoded RNase III autoregulates its expression and suppresses RNA interference-mediated gene silencing.
  J Virol, 84, 3624-3630.  
20169186 P.Parameswaran, E.Sklan, C.Wilkins, T.Burgon, M.A.Samuel, R.Lu, K.M.Ansel, V.Heissmeyer, S.Einav, W.Jackson, T.Doukas, S.Paranjape, C.Polacek, F.B.dos Santos, R.Jalili, F.Babrzadeh, B.Gharizadeh, D.Grimm, M.Kay, S.Koike, P.Sarnow, M.Ronaghi, S.W.Ding, E.Harris, M.Chow, M.S.Diamond, K.Kirkegaard, J.S.Glenn, and A.Z.Fire (2010).
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems.
  PLoS Pathog, 6, e1000764.  
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
19968858 W.M.Li, T.Barnes, and C.H.Lee (2010).
Endoribonucleases--enzymes gaining spotlight in mRNA metabolism.
  FEBS J, 277, 627-641.  
19264675 J.Xiao, C.E.Feehery, G.Tzertzinis, and C.V.Maina (2009).
E. coli RNase III(E38A) generates discrete-sized products from long dsRNA.
  RNA, 15, 984-991.  
19158786 M.Jinek, and J.A.Doudna (2009).
A three-dimensional view of the molecular machinery of RNA interference.
  Nature, 457, 405-412.  
19729508 M.L.Yeung, Y.Bennasser, K.Watashi, S.Y.Le, L.Houzet, and K.T.Jeang (2009).
Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid.
  Nucleic Acids Res, 37, 6575-6586.  
19229243 M.M.Ghodgaonkar, R.G.Shah, F.Kandan-Kulangara, E.B.Affar, H.H.Qi, E.Wiemer, and G.M.Shah (2009).
Abrogation of DNA vector-based RNAi during apoptosis in mammalian cells due to caspase-mediated cleavage and inactivation of Dicer-1.
  Cell Death Differ, 16, 858-868.  
19836333 P.W.Lau, C.S.Potter, B.Carragher, and I.J.MacRae (2009).
Structure of the human Dicer-TRBP complex by electron microscopy.
  Structure, 17, 1326-1332.  
19154332 Y.Redko, and C.Condon (2009).
Ribosomal protein L3 bound to 23S precursor rRNA stimulates its maturation by Mini-III ribonuclease.
  Mol Microbiol, 71, 1145-1154.  
18572190 A.Hernandez, A.Panigrahi, C.Cifuentes-Rojas, A.Sacharidou, K.Stuart, and J.Cruz-Reyes (2008).
Determinants for association and guide RNA-directed endonuclease cleavage by purified RNA editing complexes from Trypanosoma brucei.
  J Mol Biol, 381, 35-48.  
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
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.  
17954557 J.Carnes, J.R.Trotter, A.Peltan, M.Fleck, and K.Stuart (2008).
RNA editing in Trypanosoma brucei requires three different editosomes.
  Mol Cell Biol, 28, 122-130.  
19141481 K.S.Kim, R.Manasherob, and S.N.Cohen (2008).
YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity.
  Genes Dev, 22, 3497-3508.  
18641914 K.Zenke, and K.H.Kim (2008).
Functional characterization of the RNase III gene of rock bream iridovirus.
  Arch Virol, 153, 1651-1656.  
18337749 M.Nowotny, S.M.Cerritelli, R.Ghirlando, S.A.Gaidamakov, R.J.Crouch, and W.Yang (2008).
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
  EMBO J, 27, 1172-1181.
PDB code: 3bsu
18363798 Y.Redko, D.H.Bechhofer, and C.Condon (2008).
Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis.
  Mol Microbiol, 68, 1096-1106.  
18268334 Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, and T.L.James (2008).
Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage.
  Proc Natl Acad Sci U S A, 105, 2391-2396.
PDB codes: 3c4b 3c4t
18454937 d.o. .H.Lim, J.Kim, S.Kim, R.W.Carthew, and Y.S.Lee (2008).
Functional analysis of dicer-2 missense mutations in the siRNA pathway of Drosophila.
  Biochem Biophys Res Commun, 371, 525-530.  
17534422 B.Lamontagne, and S.Abou Elela (2007).
Short RNA guides cleavage by eukaryotic RNase III.
  PLoS ONE, 2, e472.  
17158098 C.Cifuentes-Rojas, P.Pavia, A.Hernandez, D.Osterwisch, C.Puerta, and J.Cruz-Reyes (2007).
Substrate determinants for RNA editing and editing complex interactions at a site for full-round U insertion.
  J Biol Chem, 282, 4265-4276.  
17194582 I.J.MacRae, and J.A.Doudna (2007).
Ribonuclease revisited: structural insights into ribonuclease III family enzymes.
  Curr Opin Struct Biol, 17, 138-145.  
17873886 I.J.MacRae, K.Zhou, and J.A.Doudna (2007).
Structural determinants of RNA recognition and cleavage by Dicer.
  Nat Struct Mol Biol, 14, 934-940.  
17189683 J.A.Worrall, and B.F.Luisi (2007).
Information available at cut rates: structure and mechanism of ribonucleases.
  Curr Opin Struct Biol, 17, 128-137.  
17174977 K.Calvin, and H.Li (2007).
Achieving specific RNA cleavage activity by an inactive splicing endonuclease subunit through engineered oligomerization.
  J Mol Biol, 366, 642-649.  
17459519 M.Thomas, J.J.Lu, J.Chen, and A.M.Klibanov (2007).
Non-viral siRNA delivery to the lung.
  Adv Drug Deliv Rev, 59, 124-133.  
17658285 S.U.Colmenares, S.M.Buker, M.Buhler, M.Dlakić, and D.Moazed (2007).
Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi.
  Mol Cell, 27, 449-461.  
17704815 S.Y.Sohn, W.J.Bae, J.J.Kim, K.H.Yeom, V.N.Kim, and Y.Cho (2007).
Crystal structure of human DGCR8 core.
  Nat Struct Mol Biol, 14, 847-853.
PDB code: 2yt4
17259216 T.Katoh, and T.Suzuki (2007).
Specific residues at every third position of siRNA shape its efficient RNAi activity.
  Nucleic Acids Res, 35, e27.  
17369311 V.K.Babbarwal, M.Fleck, N.L.Ernst, A.Schnaufer, and K.Stuart (2007).
An essential role of KREPB4 in RNA editing and structural integrity of the editosome in Trypanosoma brucei.
  RNA, 13, 737-744.  
16518387 A.Cook, and E.Conti (2006).
Dicer measures up.
  Nat Struct Mol Biol, 13, 190-192.  
16896014 A.V.Pertzev, and A.W.Nicholson (2006).
Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III.
  Nucleic Acids Res, 34, 3708-3721.  
16957732 C.Frazão, C.E.McVey, M.Amblar, A.Barbas, C.Vonrhein, C.M.Arraiano, and M.A.Carrondo (2006).
Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex.
  Nature, 443, 110-114.
PDB codes: 2ix0 2ix1
17381284 D.J.Patel, J.B.Ma, Y.R.Yuan, K.Ye, Y.Pei, V.Kuryavyi, L.Malinina, G.Meister, and T.Tuschl (2006).
Structural biology of RNA silencing and its functional implications.
  Cold Spring Harb Symp Quant Biol, 71, 81-93.  
17053086 H.Shi, C.Tschudi, and E.Ullu (2006).
An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei.
  RNA, 12, 2063-2072.  
17381283 I.J.Macrae, F.Li, K.Zhou, W.Z.Cande, and J.A.Doudna (2006).
Structure of Dicer and mechanistic implications for RNAi.
  Cold Spring Harb Symp Quant Biol, 71, 73-80.  
16954143 M.Dlakić (2006).
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold.
  Bioinformatics, 22, 2711-2714.  
16927374 R.E.Collins, and X.Cheng (2006).
Structural and biochemical advances in mammalian RNAi.
  J Cell Biochem, 99, 1251-1266.  
16600865 W.Yang, J.Y.Lee, and M.Nowotny (2006).
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
  Mol Cell, 22, 5.  
16855311 X.Ji (2006).
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
  Acta Crystallogr D Biol Crystallogr, 62, 933-940.  
16963561 X.Kang, G.Gao, K.Rogers, A.M.Falick, S.Zhou, and L.Simpson (2006).
Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins.
  Proc Natl Acad Sci U S A, 103, 13944-13949.  
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.