Difference between revisions of "RnpB"

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* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2A64 2A64] (from Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1NBS 1NBS] (specificity domain)
 
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2A64 2A64] (from Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1NBS 1NBS] (specificity domain)
  
 +
 +
= Categories containing this gene/protein =
 +
{{SubtiWiki category|[[Rnases]]}},
 +
{{SubtiWiki category|[[translation]]}},
 +
{{SubtiWiki category|[[ncRNA]]}}
 
=The RNA=
 
=The RNA=
  

Revision as of 19:23, 30 November 2010

  • Description: RNA component of RNase P

Gene name rnpB
Synonyms rnaP
Essential no
Product RNA component of ribonuclease P
(RNase P) (catalytic subunit, ribozyme)
Function cleavage of precursor sequences
from the 5' ends of pre-tRNAs
Gene length 401 bp
Immediate neighbours ypsC, ypsB
Gene sequence (+200bp)
Genetic context
RnpB context.gif
This image was kindly provided by SubtiList








The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]
  • Structure: 2A64 (from Geobacillus stearothermophilus), 1NBS (specificity domain)


Categories containing this gene/protein

Rnases, translation, ncRNA

The RNA

  • Biological activity: 5' end maturation of precursor tRNAs
  • RNA family:
  • cofactor: divalent cations (Ca(II) or Mg (II)) for the stabilization of the complex with pre-tRNA PubMed
  • interaction: RnpA-RnpB

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/RNA

Your additional remarks

References

Reviews

Roland K Hartmann, Markus Gössringer, Bettina Späth, Susan Fischer, Anita Marchfelder
The making of tRNAs and more - RNase P and tRNase Z.
Prog Mol Biol Transl Sci: 2009, 85;319-68
[PubMed:19215776] [WorldCat.org] [DOI] (P p)

J Kristin Smith, John Hsieh, Carol A Fierke
Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis.
Biopolymers: 2007, 87(5-6);329-38
[PubMed:17868095] [WorldCat.org] [DOI] (P p)

Alexei V Kazantsev, Norman R Pace
Bacterial RNase P: a new view of an ancient enzyme.
Nat Rev Microbiol: 2006, 4(10);729-40
[PubMed:16980936] [WorldCat.org] [DOI] (I p)

Donald Evans, Steven M Marquez, Norman R Pace
RNase P: interface of the RNA and protein worlds.
Trends Biochem Sci: 2006, 31(6);333-41
[PubMed:16679018] [WorldCat.org] [DOI] (P p)

Alfredo Torres-Larios, Kerren K Swinger, Tao Pan, Alfonso Mondragón
Structure of ribonuclease P--a universal ribozyme.
Curr Opin Struct Biol: 2006, 16(3);327-35
[PubMed:16650980] [WorldCat.org] [DOI] (P p)

John Hsieh, Andy J Andrews, Carol A Fierke
Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
Biopolymers: 2004, 73(1);79-89
[PubMed:14691942] [WorldCat.org] [DOI] (P p)

Enno Hartmann, Roland K Hartmann
The enigma of ribonuclease P evolution.
Trends Genet: 2003, 19(10);561-9
[PubMed:14550630] [WorldCat.org] [DOI] (P p)


Original Publications

Ruiting Liang, Elzbieta Kierzek, Ryszard Kierzek, Douglas H Turner
Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain.
Biochemistry: 2010, 49(37);8155-68
[PubMed:20557101] [WorldCat.org] [DOI] (I p)

John Hsieh, Kristin S Koutmou, David Rueda, Markos Koutmos, Nils G Walter, Carol A Fierke
A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P.
J Mol Biol: 2010, 400(1);38-51
[PubMed:20434461] [WorldCat.org] [DOI] (I p)

Nathan J Baird, Haipeng Gong, Syed S Zaheer, Karl F Freed, Tao Pan, Tobin R Sosnick
Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.
J Mol Biol: 2010, 397(5);1298-306
[PubMed:20188108] [WorldCat.org] [DOI] (I p)

Kristin S Koutmou, Anette Casiano-Negroni, Melissa M Getz, Samuel Pazicni, Andrew J Andrews, James E Penner-Hahn, Hashim M Al-Hashimi, Carol A Fierke
NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.
Proc Natl Acad Sci U S A: 2010, 107(6);2479-84
[PubMed:20133747] [WorldCat.org] [DOI] (I p)

Kristin S Koutmou, Nathan H Zahler, Jeffrey C Kurz, Frank E Campbell, Michael E Harris, Carol A Fierke
Protein-precursor tRNA contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease P.
J Mol Biol: 2010, 396(1);195-208
[PubMed:19932118] [WorldCat.org] [DOI] (I p)

Stefanie A Mortimer, Kevin M Weeks
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain.
Proc Natl Acad Sci U S A: 2009, 106(37);15622-7
[PubMed:19717440] [WorldCat.org] [DOI] (I p)

John Hsieh, Carol A Fierke
Conformational change in the Bacillus subtilis RNase P holoenzyme--pre-tRNA complex enhances substrate affinity and limits cleavage rate.
RNA: 2009, 15(8);1565-77
[PubMed:19549719] [WorldCat.org] [DOI] (I p)

Barbara Wegscheid, Roland K Hartmann
In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3'-CCA.
Nucleic Acids Res: 2007, 35(6);2060-73
[PubMed:17355991] [WorldCat.org] [DOI] (I p)

Somashekarappa Niranjanakumari, Jeremy J Day-Storms, Mahiuddin Ahmed, John Hsieh, Nathan H Zahler, Ronald A Venters, Carol A Fierke
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.
RNA: 2007, 13(4);521-35
[PubMed:17299131] [WorldCat.org] [DOI] (P p)

Barbara Wegscheid, Ciarán Condon, Roland K Hartmann
Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences.
EMBO Rep: 2006, 7(4);411-7
[PubMed:16470227] [WorldCat.org] [DOI] (P p)

Tomoaki Ando, Terumichi Tanaka, Yo Kikuchi
Bacterial ribonuclease P reaction is affected by substrate shape and magnesium ion concentration.
Nucleic Acids Res Suppl: 2003, (3);293-4
[PubMed:14510496] [DOI] (P p)

Tomoaki Ando, Terumichi Tanaka, Yo Kikuchi
Comparative analyses of hairpin substrate recognition by Escherichia coli and Bacillus subtilis ribonuclease P ribozymes.
Biosci Biotechnol Biochem: 2003, 67(8);1825-7
[PubMed:12951523] [WorldCat.org] [DOI] (P p)

Y Hori, T Tanaka, Y Kikuchi
In vitro hyperprocessing of tRNAs by Bacillus subtilis ribonuclease P RNA.
Nucleic Acids Res Suppl: 2001, (1);209-10
[PubMed:12836338] [DOI] (P p)

Christoph Rox, Ralph Feltens, Thomas Pfeiffer, Roland K Hartmann
Potential contact sites between the protein and RNA subunit in the Bacillus subtilis RNase P holoenzyme.
J Mol Biol: 2002, 315(4);551-60
[PubMed:11812129] [WorldCat.org] [DOI] (P p)

Y Hori, E Sakai, T Tanaka, Y Kikuchi
Hyperprocessing reaction of tRNA by Bacillus subtilis ribonuclease P ribozyme.
FEBS Lett: 2001, 505(2);337-9
[PubMed:11577704] [WorldCat.org] [DOI] (P p)

A Hansen, T Pfeiffer, T Zuleeg, S Limmer, J Ciesiolka, R Feltens, R K Hartmann
Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzymes from Escherichia coli and Bacillus subtilis.
Mol Microbiol: 2001, 41(1);131-43
[PubMed:11454206] [WorldCat.org] [DOI] (P p)

J M Warnecke, R Held, S Busch, R K Hartmann
Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis.
J Mol Biol: 1999, 290(2);433-45
[PubMed:10390342] [WorldCat.org] [DOI] (P p)

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