spacer
spacer
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2zae
Jmol
Contents
Protein chains
105 a.a. *
98 a.a. *
Ligands
NO3 ×9
GOL ×4
Metals
_ZN ×2
Waters ×179
* Residue conservation analysis
PDB id:
2zae
Name: Hydrolase
Title: Crystal structure of protein ph1601p in complex with protein of archaeal ribonuclease p from pyrococcus horikoshii ot3
Structure: Ribonuclease p protein component 1. Chain: a, c. Synonym: rnase p component 1. Engineered: yes. Ribonuclease p protein component 4. Chain: b, d. Synonym: rnase p component 4. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3. Gene: rnp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rnp4.
Resolution:
2.21Å     R-factor:   0.202     R-free:   0.250
Authors: T.Honda,Y.Kakuta,M.Kimura
Key ref:
T.Honda et al. (2008). Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P. J Mol Biol, 384, 652-662. PubMed id: 18929577 DOI: 10.1016/j.jmb.2008.09.056
Date:
04-Oct-07     Release date:   14-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O59425  (RNP1_PYRHO) -  Ribonuclease P protein component 1
Seq:
Struc: 		127 a.a.
105 a.a.*
Protein chains
Pfam   ArchSchema ?
O59248  (RNP4_PYRHO) -  Ribonuclease P protein component 4
Seq:
Struc: 		120 a.a.
98 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: 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   4 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1016/j.jmb.2008.09.056 J Mol Biol 384:652-662 (2008)
PubMed id: 18929577  
 
 
Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P.
T.Honda, Y.Kakuta, K.Kimura, J.Saho, M.Kimura.
 
  ABSTRACT  
 
Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5'-leader sequence of precursor tRNA. Human RNase P protein subunits Rpp21 and Rpp29, which bind to each other, with catalytic RNA (H1 RNA) are sufficient for activating endonucleolytic cleavage of precursor tRNA. Here we have determined the crystal structure of the complex between the Pyrococcus horikoshii RNase P proteins PhoRpp21 and PhoRpp29, the archaeal homologs of Rpp21 and Rpp29, respectively. PhoRpp21 and PhoRpp29 form a heterodimeric structure where the two N-terminal helices (alpha1 and alpha2) in PhoRpp21 predominantly interact with the N-terminal extended structure, the beta-strand (beta2), and the C-terminal helix (alpha3) in PhoRpp29. The interface is dominated by hydrogen bonds and several salt bridges, rather than hydrophobic interactions. The electrostatic potential on the surface of the heterodimer shows a positively charged cluster on one face, suggesting a possible RNA-binding surface of the PhoRpp21-PhoRpp29 complex. The present structure, along with the result of a mutational analysis, suggests that heterodimerization between PhoRpp21 and PhoRpp29 plays an important role in the function of P. horikoshii RNase P.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Interfaces for the protein–protein interactions. (a) The surface representation of the interface of PhoRpp29 and PhoRpp21 is shown. Surfaces are colored according to their electrostatic potential as calculated by the program GRASP.^26 The surface potential is displayed as a color gradient from red (negative) to blue (positive), showing a high degree of charge complementarity. (b) The hydrogen-bonding network at the interface for the N-terminal extended structure of PhoRpp29 with the N-terminal helices in PhoRpp21. (c) The interface between the central β-strand β2 in PhoRpp29 and the N-terminal helices in PhoRpp21. (d) The interfaces between the C-terminal helix (α3) in PhoRpp29 and the N-terminal helices in PhoRpp21. The amino acid side chains located at N-terminal helices α1 and α2 in PhoRpp21 are shown in violet and blue, respectively, and those at the N-terminal extended structure, β-strand (β2), and C-terminal helix (α3) in PhoRpp29 are shown in yellow, orange, and green, respectively. The amino acid residues in PhoRpp21 and PhoRpp29 are written in red and black, respectively. 		Figure 3.
Fig. 3. Electrostatic surface potentials of the PhoRpp21–PhoRpp29 complex. The crystal structure of the protein complex is shown at the top, and the corresponding surface potentials are shown at the bottom. Each view is rotated by 90°.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 652-662) copyright 2008.  
  Figures were selected by an automated process.  

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
20215441 K.L.Hands-Taylor, L.Martino, R.Tata, J.J.Babon, T.T.Bui, A.F.Drake, R.L.Beavil, G.J.Pruijn, P.R.Brown, and M.R.Conte (2010).
Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA.
  Nucleic Acids Res, 38, 4052-4066.  
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.  
20139624 S.Kosaka, K.Hada, T.Nakashima, and M.Kimura (2010).
Structural changes in ribonuclease P RNA in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 induced on interaction with proteins.
  Biosci Biotechnol Biochem, 74, 394-396.  
20139629 T.Honda, T.Hara, J.Nan, X.Zhang, and M.Kimura (2010).
Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 work on distinct functional domains of the RNA subunit.
  Biosci Biotechnol Biochem, 74, 266-273.  
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
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.