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Hydrolase PDB id
1tsf
Jmol
Contents
Protein chain
81 a.a. *
Waters ×99
* Residue conservation analysis
PDB id:
1tsf
Name: Hydrolase
Title: Crystal structure of the archaeal homolog of human rnase p protein rpp29 from archaeoglobus fulgidus
Structure: Ribonuclease p protein component 1. Chain: a. Synonym: rnase p component 1, arpp29. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: rnp1, af1917. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Fusion.
Resolution:
1.70Å     R-factor:   0.250     R-free:   0.283
Authors: D.J.Sidote,J.Heideker,D.W.Hoffman
Key ref:
D.J.Sidote et al. (2004). Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus. Biochemistry, 43, 14128-14138. PubMed id: 15518563 DOI: 10.1021/bi048578z
Date:
21-Jun-04     Release date:   12-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O28362  (RNP1_ARCFU) -  Ribonuclease P protein component 1
Seq:
Struc: 		102 a.a.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Cellular component     ribonuclease P complex   2 terms 
  Biological process     rRNA processing   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1021/bi048578z Biochemistry 43:14128-14138 (2004)
PubMed id: 15518563  
 
 
Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus.
D.J.Sidote, J.Heideker, D.W.Hoffman.
 
  ABSTRACT  
 
The crystal structure of ribonuclease P protein aRpp29 from the sulfate-reducing hyperthermophile Archaeoglobus fulgidus was determined at 1.7 A resolution using X-ray diffraction methods. The central feature of this archaeal protein is a sheet of six antiparallel beta-strands twisted around a conserved hydrophobic core. Residues near the N- and C-termini form helical structures that are oriented in an antiparallel manner. A comparison of conserved amino acids indicates that archaeal aRpp29 is homologous to human ribonuclease P protein Rpp29. The aRpp29 protein is structurally similar to bacterial transcription factors Hfq and NusG, as well as the Sm and Sm-like RNA-associated proteins from eukarya. The crystal structure of A. fulgidus aRpp29 differs from the previously reported solution structure, where NMR data did not detect the helices and indicated that approximately 40% of the residues are relatively flexible or disordered. Circular dichroism data indicate that the protein has less helical content than the amount observed in the crystal, suggesting that in solution the helical regions are unfolded or in equilibrium between folded and unfolded forms; this hypothesis is consistent with amide proton exchange rate data. Surface residues that are conserved from archaea to humans and are likely to interact with the ribonuclease P RNA or other protein subunits are identified in the structure. The model of the aRpp29 protein defined by this work provides an essential step toward eventually understanding the overall architecture of ribonuclease P.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
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.  
16418270 R.C.Wilson, C.J.Bohlen, M.P.Foster, and C.E.Bell (2006).
Structure of Pfu Pop5, an archaeal RNase P protein.
  Proc Natl Acad Sci U S A, 103, 873-878.
PDB code: 2av5
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.  
16618965 S.Xiao, J.Hsieh, R.L.Nugent, D.J.Coughlin, C.A.Fierke, and D.R.Engelke (2006).
Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP.
  RNA, 12, 1023-1037.  
16155184 E.Sharin, A.Schein, H.Mann, Y.Ben-Asouli, and N.Jarrous (2005).
RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis.
  Nucleic Acids Res, 33, 5120-5132.  
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.