Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.

Muroya, A.Tsuchiya, D.Ishikawa, M.Haruki, M.Morikawa, M.Kanaya, S.Morikawa, K.

(2001) Protein Sci 10: 707-714

  • DOI: https://doi.org/10.1110/ps.48001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.

  • Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIBONUCLEASE HII213Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: RNHB
Find proteins for O74035 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore O74035 
Go to UniProtKB:  O74035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74035
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.54α = 90
b = 72.99β = 90
c = 78.32γ = 90
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: 2001-04-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references