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RNA binding protein PDB id
1pc0
Jmol
Contents
Protein chain
61 a.a. *
* Residue conservation analysis
PDB id:
1pc0
Name: RNA binding protein
Title: Nmr structure of the archaeal homologue of rnase p protein rpp29
Structure: Hypothetical protein af1917. Chain: a. Fragment: residue 17-77. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af1917. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 10 models
Authors: D.J.Sidote,D.W.Hoffman
Key ref:
D.J.Sidote and D.W.Hoffman (2003). NMR structure of an archaeal homologue of ribonuclease P protein Rpp29. Biochemistry, 42, 13541-13550. PubMed id: 14622001 DOI: 10.1021/bi030170z
Date:
15-May-03     Release date:   09-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O28362  (RNP1_ARCFU) -  Ribonuclease P protein component 1
Seq:
Struc: 		102 a.a.
61 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     RNA binding     2 terms  

 

 
DOI no: 10.1021/bi030170z Biochemistry 42:13541-13550 (2003)
PubMed id: 14622001  
 
 
NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.
D.J.Sidote, D.W.Hoffman.
 
  ABSTRACT  
 
A protein component of the Archaeoglobus fulgidus RNase P was expressed in Escherichia coli, purified, and structurally characterized using multidimensional NMR methods. The dominant structural feature of this 11 kDa protein is a sheet of six antiparallel beta-strands, wrapped around a core of conserved hydrophobic amino acids. Amide proton exchange and (15)N relaxation rate data provide evidence that the first 16 residues of the protein, located before the start of the first beta-strand, and the last 24 residues, located past the end of the last beta-strand, are relatively flexible; this contrasts with the relatively rigid and well-defined structure of the beta-sheet. Amino acid sequence comparisons among a diverse set of species indicate that the A. fulgidus protein is homologous to the human RNase P protein Rpp29, yeast RNase P protein Pop4, and a known archaeal RNase P protein from Methanobacter thermoautotrophicus; conserved hydrophobic residues indicate that the homologous protein in each of these species contains a similar beta-sheet structure. Conserved surface residues located in the loop connecting strands beta2 and beta3, the loop connecting strands beta4 and beta5, and in the flexible N- and C-terminal tails are most likely to have specific interactions with the RNA and other proteins of RNase P. The structural model of an RNase P protein component provided by the present work provides an essential step toward eventually understanding the overall architecture of this complex enzyme and the mechanism by which it performs its functions.
 

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.  
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.  
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
17143896 D.Monleón, M.Martínez-Vicente, V.Esteve, L.Yim, S.Prado, M.E.Armengod, and B.Celda (2007).
Structural insights into the GTPase domain of Escherichia coli MnmE protein.
  Proteins, 66, 726-739.
PDB code: 1rfl
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.  
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.  
15096576 T.J.Welting, W.J.van Venrooij, and G.J.Pruijn (2004).
Mutual interactions between subunits of the human RNase MRP ribonucleoprotein complex.
  Nucleic Acids Res, 32, 2138-2146.  
15317976 T.Numata, I.Ishimatsu, Y.Kakuta, I.Tanaka, and M.Kimura (2004).
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.
  RNA, 10, 1423-1432.
PDB code: 1v76
14673079 W.P.Boomershine, C.A.McElroy, H.Y.Tsai, R.C.Wilson, V.Gopalan, and M.P.Foster (2003).
Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.
  Proc Natl Acad Sci U S A, 100, 15398-15403.
PDB code: 1oqk
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.