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PDBsum entry 1i4s

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protein Protein-protein interface(s) links
Hydrolase PDB id
1i4s
Jmol
Contents
Protein chains
147 a.a. *
Waters ×252
* Residue conservation analysis
PDB id:
1i4s
Name: Hydrolase
Title: Crystal structure of rnase iii endonuclease domain from aquifex aeolicus at 2.15 angstrom resolution
Structure: Ribonuclease iii. Chain: a, b. Fragment: n-terminal endonuclease domain. Synonym: rnase iii. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.15Å     R-factor:   0.222     R-free:   0.275
Authors: J.Blaszczyk,X.Ji
Key ref:
J.Blaszczyk et al. (2001). Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure, 9, 1225-1236. PubMed id: 11738048 DOI: 10.1016/S0969-2126(01)00685-2
Date:
22-Feb-01     Release date:   19-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67082  (RNC_AQUAE) -  Ribonuclease 3
Seq:
Struc:
221 a.a.
147 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     RNA processing   2 terms 
  Biochemical function     RNA binding     2 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00685-2 Structure 9:1225-1236 (2001)
PubMed id: 11738048  
 
 
Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.
J.Blaszczyk, J.E.Tropea, M.Bubunenko, K.M.Routzahn, D.S.Waugh, D.L.Court, X.Ji.
 
  ABSTRACT  
 
BACKGROUND: Aquifex aeolicus Ribonuclease III (Aa-RNase III) belongs to the family of Mg(2+)-dependent endonucleases that show specificity for double-stranded RNA (dsRNA). RNase III is conserved in all known bacteria and eukaryotes and has 1-2 copies of a 9-residue consensus sequence, known as the RNase III signature motif. The bacterial RNase III proteins are the simplest, consisting of two domains: an N-terminal endonuclease domain, followed by a double-stranded RNA binding domain (dsRBD). The three-dimensional structure of the dsRBD in Escherichia coli RNase III has been elucidated; no structural information is available for the endonuclease domain of any RNase III. RESULTS: We present the crystal structures of the Aa-RNase III endonuclease domain in its ligand-free form and in complex with Mn(2+). The structures reveal a novel protein fold and suggest a mechanism for dsRNA cleavage. On the basis of structural, genetic, and biological data, we have constructed a hypothetical model of Aa-RNase III in complex with dsRNA and Mg(2+) ion, which provides the first glimpse of RNase III in action. CONCLUSIONS: The functional Aa-RNase III dimer is formed via mainly hydrophobic interactions, including a "ball-and-socket" junction that ensures accurate alignment of the two monomers. The fold of the polypeptide chain and its dimerization create a valley with two compound active centers at each end of the valley. The valley can accommodate a dsRNA substrate. Mn(2+) binding has significant impact on crystal packing, intermolecular interactions, thermal stability, and the formation of two RNA-cutting sites within each compound active center.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Structure of the Ligand-free Dimer of Aa-RNase III Endonuclease Domain(a) Dimer interface of Aa-RNase III. Molecule A is illustrated as a surface representation with positive and negative potentials indicated by blue and red, respectively. Molecule B is represented as a backbone "worm" with a stick model for the "ball-and-socket" side chains. The secondary structure elements involved in dimerization are identified with green labels. In the upper portion of the illustration, the shape of the "socket" is shown with the stick model of F41 from Molecule B, whereas, in the lower potion, the shape of the "ball" is outlined in the middle of five side chains that form the socket (see text).(b) A ribbon diagram of molecules A (in green) and B (in blue). The secondary structure assignment is shown in molecule A only. Two sets of six active site residues are labeled, including E37, E40, D44, D107, and E110 from one molecule and E64 from the other. Each set forms a compound active center.(c) A surface representation with red and blue indicating negative and positive potentials, respectively. Notice that the valley on the surface of the dimer has one compound active center on each end of the valley. The representations were prepared using MOLSCRIPT [61], GRASP [62], and Raster3D [63].
 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1225-1236) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20978817 E.Kiyota, R.Okada, N.Kondo, A.Hiraguri, H.Moriyama, and T.Fukuhara (2011).
An Arabidopsis RNase III-like protein, AtRTL2, cleaves double-stranded RNA in vitro.
  J Plant Res, 124, 405-414.  
21162639 H.Zhang, J.M.Pompey, and U.Singh (2011).
RNA interference in Entamoeba histolytica: implications for parasite biology and gene silencing.
  Future Microbiol, 6, 103-117.  
20717561 J.W.Gaynor, B.J.Campbell, and R.Cosstick (2010).
RNA interference: a chemist's perspective.
  Chem Soc Rev, 39, 4169-4184.  
20205586 Q.Liu, and Z.Paroo (2010).
Biochemical principles of small RNA pathways.
  Annu Rev Biochem, 79, 295-319.  
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.  
19815526 K.L.Patrick, H.Shi, N.G.Kolev, K.Ersfeld, C.Tschudi, and E.Ullu (2009).
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 106, 17933-17938.  
19158786 M.Jinek, and J.A.Doudna (2009).
A three-dimensional view of the molecular machinery of RNA interference.
  Nature, 457, 405-412.  
19487243 V.De Riso, R.Raniello, F.Maumus, A.Rogato, C.Bowler, and A.Falciatore (2009).
Gene silencing in the marine diatom Phaeodactylum tricornutum.
  Nucleic Acids Res, 37, e96.  
19165215 V.N.Kim, J.Han, and M.C.Siomi (2009).
Biogenesis of small RNAs in animals.
  Nat Rev Mol Cell Biol, 10, 126-139.  
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.  
18641914 K.Zenke, and K.H.Kim (2008).
Functional characterization of the RNase III gene of rock bream iridovirus.
  Arch Virol, 153, 1651-1656.  
18158302 P.Comella, F.Pontvianne, S.Lahmy, F.Vignols, N.Barbezier, A.Debures, E.Jobet, E.Brugidou, M.Echeverria, and J.Sáez-Vásquez (2008).
Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis.
  Nucleic Acids Res, 36, 1163-1175.  
17705269 P.Rezácová, D.Borek, S.F.Moy, A.Joachimiak, and Z.Otwinowski (2008).
Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus.
  Proteins, 70, 311-319.
PDB codes: 2fcj 2i5r
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.  
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.  
17704568 I.J.MacRae, and J.A.Doudna (2007).
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer.
  Acta Crystallogr D Biol Crystallogr, 63, 993-999.
PDB code: 2qvw
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.  
16847892 A.Fjose, and O.Drivenes (2006).
RNAi and microRNAs: from animal models to disease therapy.
  Birth Defects Res C Embryo Today, 78, 150-171.  
16611942 A.K.Panigrahi, N.L.Ernst, G.J.Domingo, M.Fleck, R.Salavati, and K.D.Stuart (2006).
Compositionally and functionally distinct editosomes in Trypanosoma brucei.
  RNA, 12, 1038-1049.  
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.  
  16582496 D.Takeshita, S.Zenno, W.C.Lee, K.Nagata, K.Saigo, and M.Tanokura (2006).
Crystallization and preliminary X-ray analysis of the C-terminal RNase III domain of human Dicer.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 402-404.  
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.  
16410517 I.J.Macrae, K.Zhou, F.Li, A.Repic, A.N.Brooks, W.Z.Cande, P.D.Adams, and J.A.Doudna (2006).
Structural basis for double-stranded RNA processing by Dicer.
  Science, 311, 195-198.
PDB code: 2ffl
16527750 J.B.Preall, Z.He, J.M.Gorra, and E.J.Sontheimer (2006).
Short interfering RNA strand selection is independent of dsRNA processing polarity during RNAi in Drosophila.
  Curr Biol, 16, 530-535.  
16439209 J.Gan, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2006).
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.
  Cell, 124, 355-366.
PDB code: 2ez6
16751099 J.Han, Y.Lee, K.H.Yeom, J.W.Nam, I.Heo, J.K.Rhee, S.Y.Sohn, Y.Cho, B.T.Zhang, and V.N.Kim (2006).
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex.
  Cell, 125, 887-901.  
16611236 R.A.Zambon, V.N.Vakharia, and L.P.Wu (2006).
RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster.
  Cell Microbiol, 8, 880-889.  
16855311 X.Ji (2006).
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
  Acta Crystallogr D Biol Crystallogr, 62, 933-940.  
17381280 Y.Lee, J.Han, K.H.Yeom, H.Jin, and V.N.Kim (2006).
Drosha in primary microRNA processing.
  Cold Spring Harb Symp Quant Biol, 71, 51-57.  
15781462 A.Best, L.Handoko, E.Schlüter, and H.U.Göringer (2005).
In vitro synthesized small interfering RNAs elicit RNA interference in african trypanosomes: an in vitro and in vivo analysis.
  J Biol Chem, 280, 20573-20579.  
16155207 D.L.Akey, and J.M.Berger (2005).
Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A.
  Protein Sci, 14, 2744-2750.
PDB code: 2a11
16269544 J.Carnes, J.R.Trotter, N.L.Ernst, A.Steinberg, and K.Stuart (2005).
An essential RNase III insertion editing endonuclease in Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 102, 16614-16619.  
15890961 J.F.Kreuze, E.I.Savenkov, W.Cuellar, X.Li, and J.P.Valkonen (2005).
Viral class 1 RNase III involved in suppression of RNA silencing.
  J Virol, 79, 7227-7238.  
16216575 J.Gan, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2005).
Intermediate states of ribonuclease III in complex with double-stranded RNA.
  Structure, 13, 1435-1442.
PDB codes: 1yyk 1yyo 1yyw 1yz9
16285922 J.R.Trotter, N.L.Ernst, J.Carnes, B.Panicucci, and K.Stuart (2005).
A deletion site editing endonuclease in Trypanosoma brucei.
  Mol Cell, 20, 403-412.  
15645515 P.A.Beal (2005).
Duplex RNA-binding enzymes: headliners from neurobiology, virology, and development.
  Chembiochem, 6, 257-266.  
15852042 V.N.Kim (2005).
MicroRNA biogenesis: coordinated cropping and dicing.
  Nat Rev Mol Cell Biol, 6, 376-385.  
15925505 W.Filipowicz, L.Jaskiewicz, F.A.Kolb, and R.S.Pillai (2005).
Post-transcriptional gene silencing by siRNAs and miRNAs.
  Curr Opin Struct Biol, 15, 331-341.  
15699182 W.Sun, A.Pertzev, and A.W.Nicholson (2005).
Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis.
  Nucleic Acids Res, 33, 807-815.  
15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
15062073 A.Pastore (2004).
How an enzyme can be a non-enzyme.
  Structure, 12, 520-521.  
14581474 B.Lamontagne, and S.A.Elela (2004).
Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage.
  J Biol Chem, 279, 2231-2241.  
15145345 E.P.Murchison, and G.J.Hannon (2004).
miRNAs on the move: miRNA biogenesis and the RNAi machinery.
  Curr Opin Cell Biol, 16, 223-229.  
15242644 H.Zhang, F.A.Kolb, L.Jaskiewicz, E.Westhof, and W.Filipowicz (2004).
Single processing center models for human Dicer and bacterial RNase III.
  Cell, 118, 57-68.  
15016361 J.Blaszczyk, J.Gan, J.E.Tropea, D.L.Court, D.S.Waugh, and X.Ji (2004).
Noncatalytic assembly of ribonuclease III with double-stranded RNA.
  Structure, 12, 457-466.
PDB codes: 1rc5 1rc7
15260964 J.W.Pham, and E.J.Sontheimer (2004).
The Making of an siRNA.
  Mol Cell, 15, 163-164.  
15211354 L.He, and G.J.Hannon (2004).
MicroRNAs: small RNAs with a big role in gene regulation.
  Nat Rev Genet, 5, 522-531.  
15104896 L.V.Ravichandran, N.M.Dean, and E.G.Marcusson (2004).
Use of antisense oligonucleotides in functional genomics and target validation.
  Oligonucleotides, 14, 49-64.  
14983173 M.A.Carmell, and G.J.Hannon (2004).
RNase III enzymes and the initiation of gene silencing.
  Nat Struct Mol Biol, 11, 214-218.  
15090619 M.Catala, B.Lamontagne, S.Larose, G.Ghazal, and S.A.Elela (2004).
Cell cycle-dependent nuclear localization of yeast RNase III is required for efficient cell division.
  Mol Biol Cell, 15, 3015-3030.  
15192703 N.Leulliot, S.Quevillon-Cheruel, M.Graille, H.van Tilbeurgh, T.C.Leeper, K.S.Godin, T.E.Edwards, S.T.Sigurdsson, N.Rozenkrants, R.J.Nagel, M.Ares, and G.Varani (2004).
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.
  EMBO J, 23, 2468-2477.
PDB codes: 1t4n 1t4o
14993466 P.Pancoska, Z.Moravek, and U.M.Moll (2004).
Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA.
  Nucleic Acids Res, 32, 1469-1479.  
15066283 Y.S.Lee, K.Nakahara, J.W.Pham, K.Kim, Z.He, E.J.Sontheimer, and R.W.Carthew (2004).
Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways.
  Cell, 117, 69-81.  
15272116 Z.He, and E.J.Sontheimer (2004).
"siRNAs and miRNAs": a meeting report on RNA silencing.
  RNA, 10, 1165-1173.  
12713903 A.M.Denli, and G.J.Hannon (2003).
RNAi: an ever-growing puzzle.
  Trends Biochem Sci, 28, 196-201.  
14602897 E.A.Worthey, A.Schnaufer, I.S.Mian, K.Stuart, and R.Salavati (2003).
Comparative analysis of editosome proteins in trypanosomatids.
  Nucleic Acids Res, 31, 6392-6408.  
14528307 E.Bernstein, S.Y.Kim, M.A.Carmell, E.P.Murchison, H.Alcorn, M.Z.Li, A.A.Mills, S.J.Elledge, K.V.Anderson, and G.J.Hannon (2003).
Dicer is essential for mouse development.
  Nat Genet, 35, 215-217.  
12711683 I.Calin-Jageman, and A.W.Nicholson (2003).
RNA structure-dependent uncoupling of substrate recognition and cleavage by Escherichia coli ribonuclease III.
  Nucleic Acids Res, 31, 2381-2392.  
12600194 J.R.Knowlton, M.Bubunenko, M.Andrykovitch, W.Guo, K.M.Routzahn, D.S.Waugh, D.L.Court, and X.Ji (2003).
A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants.
  Biochemistry, 42, 2275-2281.
PDB codes: 1npp 1npr
14665679 N.Agrawal, P.V.Dasaradhi, A.Mohmmed, P.Malhotra, R.K.Bhatnagar, and S.K.Mukherjee (2003).
RNA interference: biology, mechanism, and applications.
  Microbiol Mol Biol Rev, 67, 657-685.  
  12191433 K.R.Fortin, R.H.Nicholson, and A.W.Nicholson (2002).
Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location.
  BMC Genomics, 3, 26.  
12411504 P.Provost, D.Dishart, J.Doucet, D.Frendewey, B.Samuelsson, and O.Rådmark (2002).
Ribonuclease activity and RNA binding of recombinant human Dicer.
  EMBO J, 21, 5864-5874.  
11885596 P.D.Zamore (2001).
Thirty-three years later, a glimpse at the ribonuclease III active site.
  Mol Cell, 8, 1158-1160.  
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.