Crystal Structure of the Nanoarchaeum equitans tRNA splicing endonuclease structural subunit

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/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). 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEQ261A [auth X]153Nanoarchaeum equitansMutation(s): 0 
Gene Names: NEQ261
Find proteins for Q74MS9 (Nanoarchaeum equitans (strain Kin4-M))
Explore Q74MS9 
Go to UniProtKB:  Q74MS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74MS9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.434α = 90
b = 95.434β = 90
c = 47.791γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description