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PDBsum entry 3bk1

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protein ligands metals links
Hydrolase PDB id
3bk1
Jmol
Contents
Protein chain
551 a.a. *
Ligands
SO4 ×3
GOL ×2
Metals
_ZN ×2
Waters ×190
* Residue conservation analysis
PDB id:
3bk1
Name: Hydrolase
Title: Crystal structure analysis of rnase j
Structure: Metal dependent hydrolase. Chain: a. Fragment: unp residues 20-573. Synonym: rnase j. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Gene: ttc0775. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.33Å     R-factor:   0.197     R-free:   0.220
Authors: I.L.De La Sierra-Gallay,L.Zig,H.Putzer
Key ref:
I.L.de la Sierra-Gallay et al. (2008). Structural insights into the dual activity of RNase J. Nat Struct Mol Biol, 15, 206-212. PubMed id: 18204464 DOI: 10.1038/nsmb.1376
Date:
05-Dec-07     Release date:   22-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72JJ7  (Q72JJ7_THET2) -  Metal dependent hydrolase
Seq:
Struc:
 
Seq:
Struc:
573 a.a.
551 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1038/nsmb.1376 Nat Struct Mol Biol 15:206-212 (2008)
PubMed id: 18204464  
 
 
Structural insights into the dual activity of RNase J.
I.L.de la Sierra-Gallay, L.Zig, A.Jamalli, H.Putzer.
 
  ABSTRACT  
 
The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E-like endoribonucleolytic and a 5'-to-3' exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown. Here we report the crystal structures of Thermus thermophilus RNase J and its complex with uridine 5'-monophosphate. A binding pocket coordinating the phosphate and base moieties of the nucleotide in the vicinity of the catalytic center provide a rationale for the 5'-monophosphate-dependent 5'-to-3' exoribonucleolytic activity. We show that this dependence is strict; an initial 5'-PPP transcript cannot be degraded exonucleolytically from the 5'-end. Our results suggest that RNase J might switch promptly from endo- to exonucleolytic mode on the same RNA, a property that has important implications for RNA metabolism in numerous prokaryotic organisms and plant organelles containing RNase J orthologs.
 
  Selected figure(s)  
 
Figure 1.
(a) Structure of the RNase J monomer. The -strands and -helices are labeled, and the two zinc ions in the active site are represented as yellow spheres. The sulfate ion is shown as a stick model. The N- and C-terminal ends of the protein are indicated by the letters N and C, respectively. See Supplementary Figures 3 and 4 for the RNase J secondary structure and topology. The loops and -strands shown in red are not present in RNase Z and CPSF-73. (b) Structure of the crystallographic dimer. One monomer is drawn in the same color code as in a, the second monomer is in gray. (c) The zinc binding site for RNase J in the absence of a ligand, with a nearby complexed sulfate ion. The zinc ions are shown as yellow spheres. Ligand-mediated and hydrogen-bond interactions are indicated by dotted orange lines. (d) The catalytic center of RNase J complexed with a UMP residue. The UMP phosphate moiety is located in the site occupied by a sulfate ion in the free enzyme and is held in place by interacting with the same residues that coordinated the sulfate.
Figure 2.
(a) Comparison of the electrostatic surfaces of RNase J and RNase E. Both structures are presented with the active site facing upwards. The UMP residue and the Mg^2+ ion in the catalytic sites of RNases J and E, respectively, are indicated. (b) Topology of the C-terminal domains of RNase J and RNase E. The two domains share the same architecture, a three-stranded -sheet facing two -helices.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 206-212) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21334965 C.Condon, and D.H.Bechhofer (2011).
Regulated RNA stability in the Gram positives.
  Curr Opin Microbiol, 14, 148-154.  
21568871 L.Sun, L.Zhang, H.Zhang, and Z.G.He (2011).
Characterization of a Bifunctional β-Lactamase/Ribonuclease and Its Interaction with a Chaperone-Like Protein in the Pathogen Mycobacterium tuberculosis H37Rv.
  Biochemistry (Mosc), 76, 350-358.  
20192740 D.B.Stern, M.Goldschmidt-Clermont, and M.R.Hanson (2010).
Chloroplast RNA metabolism.
  Annu Rev Plant Biol, 61, 125-155.  
20210552 G.H.Jones (2010).
RNA degradation and the regulation of antibiotic synthesis in Streptomyces.
  Future Microbiol, 5, 419-429.  
20520623 J.G.Belasco (2010).
All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay.
  Nat Rev Mol Cell Biol, 11, 467-478.  
20025665 J.V.Bugrysheva, and J.R.Scott (2010).
The ribonucleases J1 and J2 are essential for growth and have independent roles in mRNA decay in Streptococcus pyogenes.
  Mol Microbiol, 75, 731-743.  
20696062 L.Opitz, G.Salinas-Riester, M.Grade, K.Jung, P.Jo, G.Emons, B.M.Ghadimi, T.Beissbarth, and J.Gaedcke (2010).
Impact of RNA degradation on gene expression profiling.
  BMC Med Genomics, 3, 36.  
20025672 N.Mathy, A.Hébert, P.Mervelet, L.Bénard, A.Dorléans, I.L.de la Sierra-Gallay, P.Noirot, H.Putzer, and C.Condon (2010).
Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour.
  Mol Microbiol, 75, 489-498.  
20418391 S.Yao, and D.H.Bechhofer (2010).
Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y.
  J Bacteriol, 192, 3279-3286.  
20544974 Y.Nishida, H.Ishikawa, S.Baba, N.Nakagawa, S.Kuramitsu, and R.Masui (2010).
Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
  Proteins, 78, 2395-2398.
PDB codes: 3af5 3af6
19638340 G.Deikus, and D.H.Bechhofer (2009).
Bacillus subtilis trp Leader RNA: RNase J1 endonuclease cleavage specificity and PNPase processing.
  J Biol Chem, 284, 26394-26401.  
19239894 J.Houseley, and D.Tollervey (2009).
The many pathways of RNA degradation.
  Cell, 136, 763-776.  
19779461 K.Shahbabian, A.Jamalli, L.Zig, and H.Putzer (2009).
RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis.
  EMBO J, 28, 3523-3533.  
19458035 R.Daou-Chabo, and C.Condon (2009).
RNase J1 endonuclease activity as a probe of RNA secondary structure.
  RNA, 15, 1417-1425.  
19778900 S.M.Garrey, M.Blech, J.L.Riffell, J.S.Hankins, L.M.Stickney, M.Diver, Y.H.Hsu, V.Kunanithy, and G.A.Mackie (2009).
Substrate binding and active site residues in RNases E and G: role of the 5'-sensor.
  J Biol Chem, 284, 31843-31850.  
19633085 S.Yao, and D.H.Bechhofer (2009).
Processing and stability of inducibly expressed rpsO mRNA derivatives in Bacillus subtilis.
  J Bacteriol, 191, 5680-5689.  
19850915 S.Yao, J.S.Sharp, and D.H.Bechhofer (2009).
Bacillus subtilis RNase J1 endonuclease and 5' exonuclease activities in the turnover of DeltaermC mRNA.
  RNA, 15, 2331-2339.  
19366704 T.Dutta, and M.P.Deutscher (2009).
Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease.
  J Biol Chem, 284, 15425-15431.  
19786493 T.Geissmann, C.Chevalier, M.J.Cros, S.Boisset, P.Fechter, C.Noirot, J.Schrenzel, P.François, F.Vandenesch, C.Gaspin, and P.Romby (2009).
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
  Nucleic Acids Res, 37, 7239-7257.  
19809192 T.Maeda, T.Sakai, and M.Wachi (2009).
The Corynebacterium glutamicum NCgl2281 Gene Encoding an RNase E/G family endoribonuclease can complement the Escherichia coli rng::cat mutation but not the rne-1 mutation.
  Biosci Biotechnol Biochem, 73, 2281-2286.  
18812398 G.André, S.Even, H.Putzer, P.Burguière, C.Croux, A.Danchin, I.Martin-Verstraete, and O.Soutourina (2008).
S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum.
  Nucleic Acids Res, 36, 5955-5969.  
18445592 G.Deikus, C.Condon, and D.H.Bechhofer (2008).
Role of Bacillus subtilis RNase J1 endonuclease and 5'-exonuclease activities in trp leader RNA turnover.
  J Biol Chem, 283, 17158-17167.  
18603593 M.Niemann, M.Brecht, E.Schlüter, K.Weitzel, M.Zacharias, and H.U.Göringer (2008).
TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism.
  Nucleic Acids Res, 36, 4465-4473.  
18688255 N.G.Kolev, T.A.Yario, E.Benson, and J.A.Steitz (2008).
Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.
  EMBO Rep, 9, 1013-1018.  
18493045 S.L.Zimmer, Z.Fei, and D.B.Stern (2008).
Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features.
  Genetics, 179, 125-136.  
18647167 S.Yao, J.B.Blaustein, and D.H.Bechhofer (2008).
Erythromycin-induced ribosome stalling and RNase J1-mediated mRNA processing in Bacillus subtilis.
  Mol Microbiol, 69, 1439-1449.  
18713320 U.Mäder, L.Zig, J.Kretschmer, G.Homuth, and H.Putzer (2008).
mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale.
  Mol Microbiol, 70, 183-196.  
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.