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PDBsum entry 2id0
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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2id0

 

 

 

 

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Contents
Protein chains
636 a.a. *
Metals
_MN ×4
Waters ×287
* Residue conservation analysis
PDB id:
2id0
Name: Hydrolase
Title: Escherichia coli rnase ii
Structure: Exoribonuclease 2. Chain: a, b, c, d. Synonym: exoribonuclease ii, ribonuclease ii, rnase ii. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: rnb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.35Å     R-factor:   0.227     R-free:   0.286
Authors: Y.Zuo,J.Zhang,Y.Wang,A.Malhotra
Key ref:
Y.Zuo et al. (2006). Structural basis for processivity and single-strand specificity of RNase II. Mol Cell, 24, 149-156. PubMed id: 16996291 DOI: 10.1016/j.molcel.2006.09.004
Date:
13-Sep-06     Release date:   03-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P30850  (RNB_ECOLI) -  Exoribonuclease 2 from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		644 a.a.
636 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.13.1  - exoribonuclease Ii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.

 

 
DOI no: 10.1016/j.molcel.2006.09.004 Mol Cell 24:149-156 (2006)
PubMed id: 16996291  
 
 
Structural basis for processivity and single-strand specificity of RNase II.
Y.Zuo, H.A.Vincent, J.Zhang, Y.Wang, M.P.Deutscher, A.Malhotra.
 
  ABSTRACT  
 
RNase II is a member of the widely distributed RNR family of exoribonucleases, which are highly processive 3'-->5' hydrolytic enzymes that play an important role in mRNA decay. Here, we report the crystal structure of E. coli RNase II, which reveals an architecture reminiscent of the RNA exosome. Three RNA-binding domains come together to form a clamp-like assembly, which can only accommodate single-stranded RNA. This leads into a narrow, basic channel that ends at the putative catalytic center that is completely enclosed within the body of the protein. The putative path for RNA agrees well with biochemical data indicating that a 3' single strand overhang of 7-10 nt is necessary for binding and hydrolysis by RNase II. The presence of the clamp and the narrow channel provides an explanation for the processivity of RNase II and for why its action is limited to single-stranded RNA.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. RNase II Active Center 		Figure 3.
Figure 3. Proposed Mechanism for RNase II ssRNA Specificity
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 24, 149-156) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262801 D.Schaeffer, and A.van Hoof (2011).
Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs.
  Proc Natl Acad Sci U S A, 108, 2366-2371.  
  21465561 R.G.Matos, A.Barbas, P.Gómez-Puertas, and C.M.Arraiano (2011).
Swapping the domains of exoribonucleases RNase II and RNase R: Conferring upon RNase II the ability to degrade ds RNA.
  Proteins, 79, 1853-1867.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20023028 N.Awano, V.Rajagopal, M.Arbing, S.Patel, J.Hunt, M.Inouye, and S.Phadtare (2010).
Escherichia coli RNase R has dual activities, helicase and RNase.
  J Bacteriol, 192, 1344-1352.  
20301164 R.Tomecki, K.Drazkowska, and A.Dziembowski (2010).
Mechanisms of RNA degradation by the eukaryotic exosome.
  Chembiochem, 11, 938-945.  
20531386 R.Tomecki, M.S.Kristiansen, S.Lykke-Andersen, A.Chlebowski, K.M.Larsen, R.J.Szczesny, K.Drazkowska, A.Pastula, J.S.Andersen, P.P.Stepien, A.Dziembowski, and T.H.Jensen (2010).
The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L.
  EMBO J, 29, 2342-2357.  
21091502 Z.Ge, P.Mehta, J.Richards, and A.W.Karzai (2010).
Non-stop mRNA decay initiates at the ribosome.
  Mol Microbiol, 78, 1159-1170.  
19458082 A.Barbas, R.G.Matos, M.Amblar, E.López-Viñas, P.Gomez-Puertas, and C.M.Arraiano (2009).
Determination of key residues for catalysis and RNA cleavage specificity: one mutation turns RNase II into a "SUPER-ENZYME".
  J Biol Chem, 284, 20486-20498.  
19627501 F.Garza-Sánchez, S.Shoji, K.Fredrick, and C.S.Hayes (2009).
RNase II is important for A-site mRNA cleavage during ribosome pausing.
  Mol Microbiol, 73, 882-897.  
19004832 H.A.Vincent, and M.P.Deutscher (2009).
The Roles of Individual Domains of RNase R in Substrate Binding and Exoribonuclease Activity: THE NUCLEASE DOMAIN IS SUFFICIENT FOR DIGESTION OF STRUCTURED RNA.
  J Biol Chem, 284, 486-494.  
19361424 H.A.Vincent, and M.P.Deutscher (2009).
Insights into how RNase R degrades structured RNA: analysis of the nuclease domain.
  J Mol Biol, 387, 570-583.  
19800864 M.Mamolen, and E.D.Andrulis (2009).
Characterization of the Drosophila melanogaster Dis3 ribonuclease.
  Biochem Biophys Res Commun, 390, 529-534.  
18337246 A.Barbas, R.G.Matos, M.Amblar, E.López-Viñas, P.Gomez-Puertas, and C.M.Arraiano (2008).
New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product.
  J Biol Chem, 283, 13070-13076.  
19060886 A.Lebreton, R.Tomecki, A.Dziembowski, and B.Séraphin (2008).
Endonucleolytic RNA cleavage by a eukaryotic exosome.
  Nature, 456, 993-996.  
18955140 E.Lorentzen, J.Basquin, and E.Conti (2008).
Structural organization of the RNA-degrading exosome.
  Curr Opin Struct Biol, 18, 709-713.  
18078842 H.Ibrahim, J.Wilusz, and C.J.Wilusz (2008).
RNA recognition by 3'-to-5' exonucleases: the substrate perspective.
  Biochim Biophys Acta, 1779, 256-265.  
18203924 J.M.Andrade, and C.M.Arraiano (2008).
PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins.
  RNA, 14, 543-551.  
18849432 X.Charpentier, S.P.Faucher, S.Kalachikov, and H.A.Shuman (2008).
Loss of RNase R induces competence development in Legionella pneumophila.
  J Bacteriol, 190, 8126-8136.  
17560162 C.Condon (2007).
Maturation and degradation of RNA in bacteria.
  Curr Opin Microbiol, 10, 271-278.  
17643380 C.Schneider, J.T.Anderson, and D.Tollervey (2007).
The exosome subunit Rrp44 plays a direct role in RNA substrate recognition.
  Mol Cell, 27, 324-331.  
17380189 H.Murakami, D.B.Goto, T.Toda, E.S.Chen, S.I.Grewal, R.A.Martienssen, and M.Yanagida (2007).
Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function.
  PLoS ONE, 2, e317.  
17942686 H.W.Wang, J.Wang, F.Ding, K.Callahan, M.A.Bratkowski, J.S.Butler, E.Nogales, and A.Ke (2007).
Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
  Proc Natl Acad Sci U S A, 104, 16844-16849.  
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.  
17872508 M.S.Lalonde, Y.Zuo, J.Zhang, X.Gong, S.Wu, A.Malhotra, and Z.Li (2007).
Exoribonuclease R in Mycoplasma genitalium can carry out both RNA processing and degradative functions and is sensitive to RNA ribose methylation.
  RNA, 13, 1957-1968.  
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.

 

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