Crystal structure of the Ribonuclease H1 from Chlorobium tepidum

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues.

Ratcliff, K.Corn, J.Marqusee, S.

(2009) Biochemistry 48: 5890-5898

  • DOI: https://doi.org/10.1021/bi900305p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. Pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a protein's energy landscape that lead to such thermostability. Previous studies of bacterial ribonucleases H (RNases H) from the thermophile Thermus thermophilus and the mesophile Escherichia coli revealed that the thermostability arises in part from an unusually low change in heat capacity upon unfolding (DeltaC(p)) for the thermophilic protein [Hollien, J., and Marqusee, S. (1999) Biochemistry 38, 3831-3836]. Here, we have further examined how nearly identical proteins can adapt to different thermal constraints by adding a moderately thermophilic homologue to the previously characterized mesophilic and thermophilic pair. We identified a putative RNase H from Chlorobium. tepidum and demonstrated that it is an active RNase H and adopts the RNase H fold. The moderately thermophilic protein has a melting temperature (T(m)) similar to that of the mesophilic homologue yet also has a surprisingly low DeltaC(p), like the thermophilic homologue. This new RNase H folds through a pathway similar to that of the previously studied RNases H. These results suggest that lowering the DeltaC(p) may be a general strategy for achieving thermophilicity for some protein families and implicate the folding core as the major contributor to this effect. It should now be possible to design RNases H that display the desired thermophilic or mesophilic properties, as defined by their DeltaC(p) values, and therefore fine-tune the energy landscape in a predictable fashion.

  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rnh (Ribonuclease H)
A, B
146Chlorobaculum tepidumMutation(s): 3 
Gene Names: CT1612rnhrnhA
Find proteins for Q93SU7 (Chlorobaculum tepidum)
Explore Q93SU7 
Go to UniProtKB:  Q93SU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93SU7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.457α = 100.38
b = 33.388β = 99.43
c = 66.072γ = 90.82
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection