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Hydrolase PDB id
2av5
Jmol
Contents
Protein chains
106 a.a. *
* Residue conservation analysis
PDB id:
2av5
Name: Hydrolase
Title: Crystal structure of pyrococcus furiosus pop5, an archaeal ribonuclease p protein
Structure: Ribonuclease p protein component 2. Chain: a, b, c, d, e. Synonym: rnase p component 2. Engineered: yes. Mutation: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: rnp2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
3.15Å     R-factor:   0.232     R-free:   0.263
Authors: R.C.Wilson,C.J.Bohlen,M.P.Foster,C.E.Bell
Key ref:
R.C.Wilson et al. (2006). Structure of Pfu Pop5, an archaeal RNase P protein. Proc Natl Acad Sci U S A, 103, 873-878. PubMed id: 16418270 DOI: 10.1073/pnas.0508004103
Date:
29-Aug-05     Release date:   24-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U151  (RNP2_PYRFU) -  Ribonuclease P protein component 2
Seq:
Struc:
120 a.a.
106 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.26.5  - Ribonuclease P.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tRNA processing   2 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1073/pnas.0508004103 Proc Natl Acad Sci U S A 103:873-878 (2006)
PubMed id: 16418270  
 
 
Structure of Pfu Pop5, an archaeal RNase P protein.
R.C.Wilson, C.J.Bohlen, M.P.Foster, C.E.Bell.
 
  ABSTRACT  
 
We have used NMR spectroscopy and x-ray crystallography to determine the three-dimensional structure of PF1378 (Pfu Pop5), one of four protein subunits of archaeal RNase P that shares a homolog in the eukaryotic enzyme. RNase P is an essential and ubiquitous ribonucleoprotein enzyme required for maturation of tRNA. In bacteria, the enzyme's RNA subunit is responsible for cleaving the single-stranded 5' leader sequence of precursor tRNA molecules (pre-tRNA), whereas the protein subunit assists in substrate binding. Although in bacteria the RNase P holoenzyme consists of one large catalytic RNA and one small protein subunit, in archaea and eukarya the enzyme contains several (>/=4) protein subunits, each of which lacks sequence similarity to the bacterial protein. The functional role of the proteins is poorly understood, as is the increased complexity in comparison to the bacterial enzyme. Pfu Pop5 has been directly implicated in catalysis by the observation that it pairs with PF1914 (Pfu Rpp30) to functionally reconstitute the catalytic domain of the RNA subunit. The protein adopts an alpha-beta sandwich fold highly homologous to the single-stranded RNA binding RRM domain. Furthermore, the three-dimensional arrangement of Pfu Pop5's structural elements is remarkably similar to that of the bacterial protein subunit. NMR spectra have been used to map the interaction of Pop5 with Pfu Rpp30. The data presented permit tantalizing hypotheses regarding the role of this protein subunit shared by archaeal and eukaryotic RNase P.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Crystal structure of Pfu Pop5. (a)2F[o] - F[c] electron density map of the -helical hairpin interface observed between neighboring molecules in the asymmetric unit, contoured at 1.0 . (b) Ribbon diagram of Pfu Pop5, colored according to secondary structure as assigned by DSSP (66). (c) Stereo view of Pfu Pop5 showing exposed aromatic and apolar side chains. Images were generated by using PYMOL (www.pymol.org).
Figure 3.
Fig. 3. Similarity of Pfu Pop5 to the bacterial RNase P protein and the RRM motif. (a) Similarity of three-dimensional structures of Pfu Pop5 (red) and the bacterial RNase P protein (gray; Bacillus subtilis; Protein Data Bank code 1A6F [PDB] ) (40); the structures were superimposed by aligning residues 31-44 in helix [1] of Pop5 with residues 60-73 in helix [2] of 1A6F. Note that the secondary structural elements are arranged in a different order: in Pfu Pop5 versus in the bacterial RNase P proteins. (b) Ribbon diagrams of Pfu Pop5 (red) and Homo sapiens U1A RRM1 (cyan; 1NU4) (44). (c) The Staphylococcus aureus RNase P protein, with sticks shown for residues identified as being involved in RNA interactions by chemical shift perturbation or crosslinking (6, 41). (d) Speculative model of Pfu Pop5 with the C-terminal helix (cyan) reoriented as for the bacterial RNase P protein, revealing the putative RNA-binding surface of Pfu Pop5. Apolar and positively charged side chains protrude from the surface of the -sheet. Such an orientation of helix [4] would allow access by single stranded RNA to the analogous aromatic and hydrophobic residues.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20075859 A.Perederina, O.Esakova, C.Quan, E.Khanova, and A.S.Krasilnikov (2010).
Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.
  EMBO J, 29, 761-769.
PDB code: 3iab
19931535 L.B.Lai, A.Vioque, L.A.Kirsebom, and V.Gopalan (2010).
Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects.
  FEBS Lett, 584, 287-296.  
20716516 N.Jarrous, and V.Gopalan (2010).
Archaeal/eukaryal RNase P: subunits, functions and RNA diversification.
  Nucleic Acids Res, 38, 7885-7894.  
20627997 O.Esakova, and A.S.Krasilnikov (2010).
Of proteins and RNA: the RNase P/MRP family.
  RNA, 16, 1725-1747.  
20705647 W.Y.Chen, D.K.Pulukkunat, I.M.Cho, H.Y.Tsai, and V.Gopalan (2010).
Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex.
  Nucleic Acids Res, 38, 8316-8327.  
19243011 L.A.Kirsebom, and S.Trobro (2009).
RNase P RNA-mediated cleavage.
  IUBMB Life, 61, 189-200.  
19844921 M.C.Marvin, and D.R.Engelke (2009).
Broadening the mission of an RNA enzyme.
  J Cell Biochem, 108, 1244-1251.  
18615715 S.Ohnishi, K.Pääkkönen, S.Koshiba, N.Tochio, M.Sato, N.Kobayashi, T.Harada, S.Watanabe, Y.Muto, P.Güntert, A.Tanaka, T.Kigawa, and S.Yokoyama (2009).
Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions.
  Proteins, 74, 133-144.
PDB code: 2e29
19733182 Y.Xu, C.D.Amero, D.K.Pulukkunat, V.Gopalan, and M.P.Foster (2009).
Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.
  J Mol Biol, 393, 1043-1055.
PDB code: 2ki7
18922021 C.D.Amero, W.P.Boomershine, Y.Xu, and M.Foster (2008).
Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner.
  Biochemistry, 47, 11704-11710.
PDB code: 2k3r
18558617 D.K.Pulukkunat, and V.Gopalan (2008).
Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis.
  Nucleic Acids Res, 36, 4172-4180.  
17868095 J.K.Smith, J.Hsieh, and C.A.Fierke (2007).
Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis.
  Biopolymers, 87, 329-338.  
17919279 M.Gösringer, and R.K.Hartmann (2007).
Function of heterologous and truncated RNase P proteins in Bacillus subtilis.
  Mol Microbiol, 66, 801-813.  
17483522 N.Jarrous, and R.Reiner (2007).
Human RNase P: a tRNA-processing enzyme and transcription factor.
  Nucleic Acids Res, 35, 3519-3524.  
17700860 S.Altman (2007).
A view of RNase P.
  Mol Biosyst, 3, 604-607.  
17881380 T.V.Aspinall, J.M.Gordon, H.J.Bennett, P.Karahalios, J.P.Bukowski, S.C.Walker, D.R.Engelke, and J.M.Avis (2007).
Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture.
  Nucleic Acids Res, 35, 6439-6450.  
16679018 D.Evans, S.M.Marquez, and N.R.Pace (2006).
RNase P: interface of the RNA and protein worlds.
  Trends Biochem Sci, 31, 333-341.  
17053064 H.Y.Tsai, D.K.Pulukkunat, W.K.Woznick, and V.Gopalan (2006).
Functional reconstitution and characterization of Pyrococcus furiosus RNase P.
  Proc Natl Acad Sci U S A, 103, 16147-16152.  
16980484 M.Gössringer, R.Kretschmer-Kazemi Far, and R.K.Hartmann (2006).
Analysis of RNase P protein (rnpA) expression in Bacillus subtilis utilizing strains with suppressible rnpA expression.
  J Bacteriol, 188, 6816-6823.  
16595295 S.C.Walker, and D.R.Engelke (2006).
Ribonuclease P: the evolution of an ancient RNA enzyme.
  Crit Rev Biochem Mol Biol, 41, 77.  
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 code is shown on the right.