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PDBsum entry 1v76
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protein ligands Protein-protein interface(s) links
RNA binding protein PDB id
1v76

 

 

 

 

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Contents
Protein chains
92 a.a. *
Ligands
SO4 ×2
Waters ×144
* Residue conservation analysis
PDB id:
1v76
Name: RNA binding protein
Title: Crystal structure of archaeal ribonuclease p protein ph1771p from pyrococcus horikoshii ot3
Structure: Rnase p protein ph1771p. Chain: a, b. Fragment: core region. Engineered: yes. Mutation: yes
Source: Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph1771. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.209     R-free:   0.257
Authors: T.Numata,Y.Kakuta,M.Kimura
Key ref: T.Numata et al. (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. PubMed id: 15317976
Date:
12-Dec-03     Release date:   05-Oct-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O59425  (RNP1_PYRHO) -  Ribonuclease P protein component 1 from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Seq:
Struc: 		127 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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.

 

 
Rna 10:1423-1432 (2004)
PubMed id: 15317976  
 
 
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.
T.Numata, I.Ishimatsu, Y.Kakuta, I.Tanaka, M.Kimura.
 
  ABSTRACT  
 
Ribonuclease P (RNase P) is the endonuclease responsible for the removal of 5' leader sequences from tRNA precursors. The crystal structure of an archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by X-ray crystallography. The structure is composed of four helices (alpha1-alpha4) and a six-stranded antiparallel beta-sheet (beta1-beta6) with a protruding beta-strand (beta7) at the C-terminal region. The strand beta7 forms an antiparallel beta-sheet by interacting with strand beta4 in a symmetry-related molecule, suggesting that strands beta4 and beta7 could be involved in protein-protein interactions with other RNase P proteins. Structural comparison showed that the beta-barrel structure of Ph1771p has a topological resemblance to those of Staphylococcus aureus translational regulator Hfq and Haloarcula marismortui ribosomal protein L21E, suggesting that these RNA binding proteins have a common ancestor and then diverged to specifically bind to their cognate RNAs. The structure analysis as well as structural comparison suggested two possible RNA binding sites in Ph1771p, one being a concave surface formed by terminal alpha-helices (alpha1-alpha4) and beta-strand beta6, where positively charged residues are clustered. A second possible RNA binding site is at a loop region connecting strands beta2 and beta3, where conserved hydrophilic residues are exposed to the solvent and interact specifically with sulfate ion. These two potential sites for RNA binding are located in close proximity. The crystal structure of Ph1771p provides insight into the structure and function relationships of archaeal and eukaryotic RNase 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.  
20627997 O.Esakova, and A.S.Krasilnikov (2010).
Of proteins and RNA: the RNase P/MRP family.
  RNA, 16, 1725-1747.  
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.  
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
18323660 K.Hada, T.Nakashima, T.Osawa, H.Shimada, Y.Kakuta, and M.Kimura (2008).
Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Biosci Biotechnol Biochem, 72, 749-758.
PDB code: 2z7c
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.  
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.  
15973057 M.Kifusa, H.Fukuhara, T.Hayashi, and M.Kimura (2005).
Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Biosci Biotechnol Biochem, 69, 1209-1212.  
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.

 

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