3IEY

Crystal Structure of the functional Nanoarchaeum equitans tRNA splicing endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease.

Mitchell, M.Xue, S.Erdman, R.Randau, L.Soll, D.Li, H.

(2009) Nucleic Acids Res 37: 5793-5802

  • DOI: 10.1093/nar/gkp537
  • Primary Citation of Related Structures:  
    3IEY, 3IF0

  • PubMed Abstract: 
  • The RNA splicing and processing endonuclease from Nanoarchaeum equitans (NEQ) belongs to the recently identified (alphabeta)(2) family of splicing endonucleases that require two different subunits for splicing activity. N. equitans splicing endonuclease comprises the catalytic subunit (NEQ205) and the structural subunit (NEQ261) ...

    The RNA splicing and processing endonuclease from Nanoarchaeum equitans (NEQ) belongs to the recently identified (alphabeta)(2) family of splicing endonucleases that require two different subunits for splicing activity. N. equitans splicing endonuclease comprises the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Here, we report the crystal structure of the functional NEQ enzyme at 2.1 A containing both subunits, as well as that of the NEQ261 subunit alone at 2.2 A. The functional enzyme resembles previously known alpha(2) and alpha(4) endonucleases but forms a heterotetramer: a dimer of two heterodimers of the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Surprisingly, NEQ261 alone forms a homodimer, similar to the previously known homodimer of the catalytic subunit. The homodimers of isolated subunits are inhibitory to heterodimerization as illustrated by a covalently linked catalytic homodimer that had no RNA cleavage activity upon mixing with the structural subunit. Detailed structural comparison reveals a more favorable hetero- than homodimerization interface, thereby suggesting a possible regulation mechanism of enzyme assembly through available subunits. Finally, the uniquely flexible active site of the NEQ endonuclease provides a possible explanation for its broader substrate specificity.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA-splicing endonucleaseA154Nanoarchaeum equitansMutation(s): 2 
Gene Names: endANEQ205
EC: 3.1.27.9 (PDB Primary Data), 4.6.1.16 (UniProt)
Find proteins for Q74MP4 (Nanoarchaeum equitans (strain Kin4-M))
Explore Q74MP4 
Go to UniProtKB:  Q74MP4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NEQ261B153Nanoarchaeum equitansMutation(s): 0 
Gene Names: NEQ261
Find proteins for Q74MS9 (Nanoarchaeum equitans (strain Kin4-M))
Explore Q74MS9 
Go to UniProtKB:  Q74MS9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.102α = 90
b = 124.102β = 90
c = 69.82γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-07-23 
  • Released Date: 2009-09-01 
  • Deposition Author(s): Mitchell, M., Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance