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PDBsum entry 1rc5
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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1rc5

 

 

 

 

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Contents
Protein chains
148 a.a. *
Metals
_MG ×4
Waters ×675
* Residue conservation analysis
PDB id:
1rc5
Name: Hydrolase
Title: Crystal structure of mg(ii)-complex of rnase iii endonuclease domain from aquifex aeolicus at 2.30 angstrom resolution
Structure: Ribonuclease iii. Chain: a, b, c, d. Fragment: n-terminal endonuclease domain (residues 1-147). Synonym: rnase iii. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc, aq_946. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.215     R-free:   0.255
Authors: J.Blaszczyk,J.Gan,X.Ji
Key ref:
J.Blaszczyk et al. (2004). Noncatalytic assembly of ribonuclease III with double-stranded RNA. Structure, 12, 457-466. PubMed id: 15016361 DOI: 10.1016/j.str.2004.02.004
Date:
03-Nov-03     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67082  (RNC_AQUAE) -  Ribonuclease 3 from Aquifex aeolicus (strain VF5)
Seq:
Struc: 		221 a.a.
148 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.

 

 
DOI no: 10.1016/j.str.2004.02.004 Structure 12:457-466 (2004)
PubMed id: 15016361  
 
 
Noncatalytic assembly of ribonuclease III with double-stranded RNA.
J.Blaszczyk, J.Gan, J.E.Tropea, D.L.Court, D.S.Waugh, X.Ji.
 
  ABSTRACT  
 
Ribonuclease III (RNase III) represents a family of double-stranded RNA (dsRNA) endonucleases. The simplest bacterial enzyme contains an endonuclease domain (endoND) and a dsRNA binding domain (dsRBD). RNase III can affect RNA structure and gene expression in either of two ways: as a dsRNA-processing enzyme that cleaves dsRNA, or as a dsRNA binding protein that binds but does not cleave dsRNA. We previously determined the endoND structure of Aquifex aeolicus RNase III (Aa-RNase III) and modeled a catalytic complex of full-length Aa-RNase III with dsRNA. Here, we present the crystal structure of Aa-RNase III in complex with dsRNA, revealing a noncatalytic assembly. The major differences between the two functional forms of RNase III.dsRNA are the conformation of the protein and the orientation and location of dsRNA. The flexibility of a 7 residue linker between the endoND and dsRBD enables the transition between these two forms.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overall Structure of Aa-E110KˇdsRNA(A) Illustration of a biological dimer of the Aa-E110KˇdsRNA complex. The crystallographically independent molecule and its symmetry mate are indicated by N-C, and N'-C', respectively. Secondary structural elements are labeled for those in dsRBD and a3 in the endoND. The endoND, dsRBD, dsRNA, endoND^sym, dsRBD^sym, and dsRNA^sym are colored yellow, green, green, cyan, blue, and blue, respectively. The RNase III signature motif at the N terminus of a3 is highlighted in red. Helices, b strands and loops are drawn as spirals, arrows, and pipes, respectively.(B) A different view of dimeric Aa-E110KˇdsRNA related to the view in (A) by a 90° rotation around the vertical axis.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 457-466) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322759 C.Andrady, S.K.Sharma, and K.A.Chester (2011).
Antibody-enzyme fusion proteins for cancer therapy.
  Immunotherapy, 3, 193-211.  
21080422 S.Yamashita, T.Nagata, M.Kawazoe, C.Takemoto, T.Kigawa, P.Güntert, N.Kobayashi, T.Terada, M.Shirouzu, M.Wakiyama, Y.Muto, and S.Yokoyama (2011).
Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein.
  Protein Sci, 20, 118-130.  
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
19022417 V.Dincbas-Renqvist, G.Pépin, M.Rakonjac, I.Plante, D.L.Ouellet, A.Hermansson, I.Goulet, J.Doucet, B.Samuelsson, O.Rådmark, and P.Provost (2009).
Human Dicer C-terminus functions as a 5-lipoxygenase binding domain.
  Biochim Biophys Acta, 1789, 99.  
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.  
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.  
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.  
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.  
16963573 E.De Gregorio, G.Silvestro, R.Venditti, M.S.Carlomagno, and P.P.Di Nocera (2006).
Structural organization and functional properties of miniature DNA insertion sequences in yersiniae.
  J Bacteriol, 188, 7876-7884.  
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
16672376 M.Xu, K.S.Wells, and R.B.Emeson (2006).
Substrate-dependent contribution of double-stranded RNA-binding motifs to ADAR2 function.
  Mol Biol Cell, 17, 3211-3220.  
16982647 S.Puthenveetil, L.Whitby, J.Ren, K.Kelnar, J.F.Krebs, and P.A.Beal (2006).
Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification.
  Nucleic Acids Res, 34, 4900-4911.  
16855311 X.Ji (2006).
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
  Acta Crystallogr D Biol Crystallogr, 62, 933-940.  
15987808 A.K.Henras, M.Sam, S.L.Hiley, H.Wu, T.R.Hughes, J.Feigon, and G.F.Chanfreau (2005).
Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III.
  RNA, 11, 1225-1237.  
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
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.  
15853796 K.Y.Chang, and A.Ramos (2005).
The double-stranded RNA-binding motif, a versatile macromolecular docking platform.
  FEBS J, 272, 2109-2117.  
15062073 A.Pastore (2004).
How an enzyme can be a non-enzyme.
  Structure, 12, 520-521.  
15573138 B.Tian, P.C.Bevilacqua, A.Diegelman-Parente, and M.B.Mathews (2004).
The double-stranded-RNA-binding motif: interference and much more.
  Nat Rev Mol Cell Biol, 5, 1013-1023.  
15589161 M.Landthaler, A.Yalcin, and T.Tuschl (2004).
The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis.
  Curr Biol, 14, 2162-2167.  
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
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.

 

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