3Q1R

Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA.

Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Pan, T., Mondragon, A.

(2010) Nature 468: 784-789

  • DOI: https://doi.org/10.1038/nature09516
  • Primary Citation of Related Structures:  
    3Q1Q, 3Q1R

  • PubMed Abstract: 

    • Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA ...

    Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.

    Organizational Affiliation: 

    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein componentB [auth A]118Thermotoga maritimaMutation(s): 0 
Gene Names: rnpA, RNPA OR TM1463, RNPB, TM_1463
EC: 3.1.26.5
UniProt
Find proteins for Q9X1H4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1H4 
Go to UniProtKB:  Q9X1H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H4
Protein Feature View
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNase P RNAA [auth B]347N/A
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
TRNA (PHE)86N/A
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Entity ID: 4
MoleculeChainsLengthOrganismImage
TRNA 5' LEADER7N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.92α = 90
b = 169.92β = 90
c = 185.53γ = 120
Software Package:
Software NamePurpose
MD2data collection
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance