Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.

Nakayama, H.Shimamura, T.Imagawa, T.Shirai, N.Itoh, T.Sako, Y.Miyano, M.Sakuraba, H.Ohshima, T.Nomura, N.Tsuge, H.

(2007) J Mol Biol 365: 362-378

  • DOI: https://doi.org/10.1016/j.jmb.2006.09.066
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel LAGLIDADG-type homing endonuclease (HEase), I-Tsp061I, from the hyperthermophilic archaeon Thermoproteus sp. IC-061 16 S rRNA gene (rDNA) intron was characterized with respect to its structure, catalytic properties and thermostability. It was found that I-Tsp061I is a HEase isoschizomer of the previously described I-PogI and exhibits the highest thermostability among the known LAGLIDADG-type HEases. Determination of the crystal structure of I-Tsp061I at 2.1 A resolution using the multiple isomorphous replacement and anomalous scattering method revealed that the overall fold is similar to that of other known LAGLIDADG-type HEases, despite little sequence similarity between I-Tsp061I and those HEases. However, I-Tsp061I contains important cross-domain polar networks, unlike its mesophilic counterparts. Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177 exists across the two packed alpha-helices containing both the LAGLIDADG catalytic motif and the GxxxG hydrophobic helix bundle motif. Another important structural feature is the salt-bridge network Asp29-Arg31-Glu182 across N and C-terminal domain interface, which appears to contribute to the stability of the domain/domain packing. On the basis of these structural analyses and extensive mutational studies, we conclude that such cross-domain polar networks play key roles in stabilizing the catalytic center and domain packing, and underlie the hyperthermostability of I-Tsp061I.

  • Organizational Affiliation

    Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative homing endonucleaseA [auth X]216ThermoproteusMutation(s): 0 
EC: 3.1
Find proteins for Q8J309 (Thermoproteus sp. IC-062)
Explore Q8J309 
Go to UniProtKB:  Q8J309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J309
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.593α = 90
b = 91.593β = 90
c = 193.643γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations